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Ethane to Methanol in Water
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===========================
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Example calculation of the difference in free energy of hydration upon
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transforming ethane into methanol with LAMMPS using *compute fep* and
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*fix adapt/fep*.
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Ethane and methanol are represented by the OPLS-AA force field (1
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molecule). Water is represented by the 3-site SPC/E model (360
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molecules).
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The strategy used to perform the alchemical transformation is the
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following:
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* The dual topology approach is used, therefore all the atoms of
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ethane and methanol are present throughout the simulation, only some
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of them are dummy sites at the endpoints of the
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transformation. Masses and intramolecular terms (bond lengths,
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angles, dihedrals) are not changed.
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* Interactions of sites that are being created (from dummy sites) or
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deleted (to become dummy sites) are treated using soft-core verions
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of the Lennard-Jones and Coulomb potentials (*pair
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lj/cut/coul/long/soft*) in order to avoid singularities. The
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exponent of the coupling parameter lambda in the soft-core pair
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potentials was in this example n = 1.
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* Eletrostatic charges that are modified are varied linearly from the
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initial to the final values. This keeps the overall charge of the
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molecule constant, which is good for the long range electrostatics
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(the coupling parameter lambda has no effect on the kspace terms).
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The following directories contain input files and results for
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calculations using free-energy perturbation (FEP), thermodynamic
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integration (TI/FDTI) and Bennet's acceptance ratio methods:
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* `mols` -- Molcule description files and force field database used to
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create the initial configurations for the simulations `data.0.lmp`
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and `data.1.lmp`
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* `fep01` -- Calculation using FEP, multi-stage transformation of an
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ethane molecule into methanol. Results in `fep01.lmp`
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* `fep10` -- Calculation using FEP, multi-stage transformation of a
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methanol molecule into ethane. Results in `fep10.lmp`
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* `fdti01` -- Calculation using FDTI, transformation of an
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ethane molecule into methanol. Results in `fdti01.lmp`
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* `fdti10` -- Calculation using FDTI, transformation of a
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methanol molecule into ethane. Results in `fdti10.lmp`
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* `bar01` -- Calculation using BAR, 1-step transformation of an
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ethane molecule into methanol. Results in `bar01.lmp`
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* `bar10` -- Calculation using BAR, 1-step transformation of a
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methanol molecule into ethane. Results in `bar10.lmp`
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The free-energy profiles can be observed by plotting the values in the
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third column of the results files. The Python scripts `fep.py`,
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`nti.py`, `fdti.py`, and `bar.py` found in the `tools` directory can
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be used to calculate the free-energy differences corresponding to the
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above transformations:
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fep.py 300 < fep01.lmp
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fep.py 300 < fep10.lmp
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nti.py 300 0.002 < fdti01.lmp
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nti.py 300 0.002 < fdti10.lmp
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fdti.py 300 0.002 < fdti01.lmp
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fdti.py 300 0.002 < fdti10.lmp
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bar.py 300 bar01.lmp bar10.lmp
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The outputs are in kcal/mol and can be compared with the experimental
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value of -6.93 kcal/mol and with simulation value from the literature:
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-6.7 kcal/mol [Jorgensen, Ravimohan, J Chem Phys 83 (1985) 3050], -6.8
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kcal/mol [Goette, Grubmüller, J Comp Chem 30 (2007) 447].
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These example calculations are for tutorial purposes only. The results
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may not be of research quality (not enough sampling, size of the step
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in lambda or of the delta for numerical derivative not optimized, no
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evaluation of ideal-gas contributions, etc.)
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File diff suppressed because it is too large
Load Diff
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@ -0,0 +1,120 @@
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# created by fftool
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units real
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boundary p p p
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atom_style full
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bond_style harmonic
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angle_style harmonic
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dihedral_style opls
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special_bonds lj/coul 0.0 0.0 0.5
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read_data data.0.lmp
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# read_restart restart.*.lmp
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# reset_timestep 0
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pair_style hybrid lj/cut/coul/long 10.0 10.0 &
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lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
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pair_modify tail no
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kspace_style pppm 1.0e-4
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pair_coeff 1 1 none # C-CO C-CO
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pair_coeff 1 2 none # C-CO C-D
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pair_coeff 1 3 none # C-CO H-D
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pair_coeff 1 4 none # C-CO H-H1
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pair_coeff 1 5 none # C-CO OHD-
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pair_coeff 1 6 none # C-CO HOD-
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pair_coeff 1 7 lj/cut/coul/long 0.0000 1.0000 # C-CO Hw
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pair_coeff 1 8 lj/cut/coul/long 0.1013 3.3286 # C-CO Ow
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pair_coeff 2 2 none # C-D C-D
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pair_coeff 2 3 none # C-D H-D
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pair_coeff 2 4 none # C-D H-H1
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pair_coeff 2 5 none # C-D OHD-
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pair_coeff 2 6 none # C-D HOD-
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pair_coeff 2 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # C-D Hw
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pair_coeff 2 8 lj/cut/coul/long/soft 0.1013 3.3286 1.0 # C-D Ow
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pair_coeff 3 3 none # H-D H-D
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pair_coeff 3 4 lj/cut/coul/long/soft 0.0300 2.5000 1.0 # H-D H-H1
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pair_coeff 3 5 none # H-D OHD-
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pair_coeff 3 6 none # H-D HOD-
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pair_coeff 3 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # H-D Hw
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pair_coeff 3 8 lj/cut/coul/long/soft 0.0683 2.8131 1.0 # H-D Ow
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pair_coeff 4 4 none # H-H1 H-H1
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pair_coeff 4 5 none # H-H1 OHD-
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pair_coeff 4 6 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # H-H1 HOD-
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pair_coeff 4 7 lj/cut/coul/long 0.0000 1.0000 # H-H1 Hw
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pair_coeff 4 8 lj/cut/coul/long 0.0683 2.8131 # H-H1 Ow
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pair_coeff 5 5 none # OHD- OHD-
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pair_coeff 5 6 none # OHD- HOD-
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pair_coeff 5 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # OHD- Hw
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pair_coeff 5 8 lj/cut/coul/long/soft 0.1625 3.1427 0.0 # OHD- Ow
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pair_coeff 6 6 none # HOD- HOD-
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pair_coeff 6 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # HOD- Hw
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pair_coeff 6 8 lj/cut/coul/long/soft 0.0000 1.7792 0.0 # HOD- Ow
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pair_coeff 7 7 lj/cut/coul/long 0.0000 1.0000 # Hw Hw
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pair_coeff 7 8 lj/cut/coul/long 0.0000 1.0000 # Hw Ow
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pair_coeff 8 8 lj/cut/coul/long 0.1554 3.1655 # Ow Ow
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variable nsteps equal 500000
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variable nprint equal ${nsteps}/500
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variable ndump equal ${nsteps}/100
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# variable nrestart equal ${nsteps}/10
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variable temp equal 300.0
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variable press equal 1.0
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neighbor 2.0 bin
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timestep 2.0
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# velocity all create ${temp} 12345
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thermo_style multi
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thermo ${nprint}
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fix fSHAKE all shake 0.0001 20 ${nprint} b 2 4 5 a 6
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fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 500
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run 100000
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reset_timestep 0
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variable dlambda equal 1.0
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variable minusdl equal -1.0
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variable dq1 equal 0.145*v_dlambda+0.180*v_dlambda
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variable dq2 equal 0.180*v_dlambda
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variable dq3 equal -0.060*v_dlambda
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variable dq4 equal 0.040*v_dlambda-0.060*v_dlambda
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variable dq5 equal -0.683*v_dlambda
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variable dq6 equal 0.418*v_dlambda
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compute cFEP all fep ${temp} &
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pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusdl &
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pair lj/cut/coul/long/soft lambda 3 4 v_minusdl &
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pair lj/cut/coul/long/soft lambda 4 6 v_dlambda &
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pair lj/cut/coul/long/soft lambda 5*6 7*8 v_dlambda &
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atom charge 1 v_dq1 &
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atom charge 2 v_dq2 &
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atom charge 3 v_dq3 &
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atom charge 4 v_dq4 &
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atom charge 5 v_dq5 &
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atom charge 6 v_dq6
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fix fFEP all ave/time 1 1 100 c_cFEP[1] c_cFEP[2] file bar01.lmp
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# compute cRDF all rdf 100 1 1
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# fix fRDF all ave/time 20 100 ${nsteps} c_cRDF file rdf.lammps mode vector
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# compute cMSD all msd
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# fix fMSD all ave/time 1 1 ${ndump} c_cMSD[1] c_cMSD[2] c_cMSD[3] c_cMSD[4] file msd.lammps
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dump dCONF all custom ${ndump} dump.lammpstrj id mol type element x y z ix iy iz
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dump_modify dCONF element C C H H O H H O
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# restart ${nrestart} restart.*.lmp
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run ${nsteps}
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write_restart restart.*.lmp
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write_data data.*.lmp
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File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
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@ -0,0 +1,120 @@
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# created by fftool
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units real
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boundary p p p
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atom_style full
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bond_style harmonic
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angle_style harmonic
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dihedral_style opls
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special_bonds lj/coul 0.0 0.0 0.5
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read_data data.1.lmp
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# read_restart restart.*.lmp
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# reset_timestep 0
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pair_style hybrid lj/cut/coul/long 10.0 10.0 &
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lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
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pair_modify tail no
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kspace_style pppm 1.0e-4
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pair_coeff 1 1 none # CO-C CO-C
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pair_coeff 1 2 none # CO-C CD-
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pair_coeff 1 3 none # CO-C HD-
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pair_coeff 1 4 none # CO-C H1-H
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pair_coeff 1 5 none # CO-C OH-D
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pair_coeff 1 6 none # CO-C HO-D
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pair_coeff 1 7 lj/cut/coul/long 0.0000 1.0000 # CO-C Hw
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pair_coeff 1 8 lj/cut/coul/long 0.1013 3.3286 # CO-C Ow
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pair_coeff 2 2 none # CD- CD-
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pair_coeff 2 3 none # CD- HD-
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pair_coeff 2 4 none # CD- H1-H
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pair_coeff 2 5 none # CD- OH-D
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pair_coeff 2 6 none # CD- HO-D
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pair_coeff 2 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # CD- Hw
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pair_coeff 2 8 lj/cut/coul/long/soft 0.1013 3.3286 0.0 # CD- Ow
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pair_coeff 3 3 none # HD- HD-
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pair_coeff 3 4 lj/cut/coul/long/soft 0.0300 2.5000 0.0 # HD- H1-H
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pair_coeff 3 5 none # HD- OH-D
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pair_coeff 3 6 none # HD- HO-D
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pair_coeff 3 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # HD- Hw
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pair_coeff 3 8 lj/cut/coul/long/soft 0.0683 2.8131 0.0 # HD- Ow
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pair_coeff 4 4 none # H1-H H1-H
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pair_coeff 4 5 none # H1-H OH-D
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pair_coeff 4 6 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # H1-H HO-D
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pair_coeff 4 7 lj/cut/coul/long 0.0000 1.0000 # H1-H Hw
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pair_coeff 4 8 lj/cut/coul/long 0.0683 2.8131 # H1-H Ow
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pair_coeff 5 5 none # OH-D OH-D
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pair_coeff 5 6 none # OH-D HO-D
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pair_coeff 5 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # OH-D Hw
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pair_coeff 5 8 lj/cut/coul/long/soft 0.1625 3.1427 1.0 # OH-D Ow
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pair_coeff 6 6 none # HO-D HO-D
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pair_coeff 6 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # HO-D Hw
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pair_coeff 6 8 lj/cut/coul/long/soft 0.0000 1.7792 1.0 # HO-D Ow
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pair_coeff 7 7 lj/cut/coul/long 0.0000 1.0000 # Hw Hw
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pair_coeff 7 8 lj/cut/coul/long 0.0000 1.0000 # Hw Ow
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pair_coeff 8 8 lj/cut/coul/long 0.1554 3.1655 # Ow Ow
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variable nsteps equal 500000
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variable nprint equal ${nsteps}/500
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variable ndump equal ${nsteps}/100
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# variable nrestart equal ${nsteps}/10
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variable temp equal 300.0
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variable press equal 1.0
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neighbor 2.0 bin
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timestep 2.0
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|
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# velocity all create ${temp} 12345
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thermo_style multi
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thermo ${nprint}
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|
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fix fSHAKE all shake 0.0001 20 ${nprint} b 2 4 5 a 6
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fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 500
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run 100000
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reset_timestep 0
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variable dlambda equal -1.0
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variable minusdl equal 1.0
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variable dq1 equal 0.145*v_dlambda+0.180*v_dlambda
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variable dq2 equal 0.180*v_dlambda
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variable dq3 equal -0.060*v_dlambda
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variable dq4 equal 0.040*v_dlambda-0.060*v_dlambda
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variable dq5 equal -0.683*v_dlambda
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variable dq6 equal 0.418*v_dlambda
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compute cFEP all fep ${temp} &
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pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusdl &
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pair lj/cut/coul/long/soft lambda 3 4 v_minusdl &
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pair lj/cut/coul/long/soft lambda 4 6 v_dlambda &
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pair lj/cut/coul/long/soft lambda 5*6 7*8 v_dlambda &
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atom charge 1 v_dq1 &
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atom charge 2 v_dq2 &
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atom charge 3 v_dq3 &
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atom charge 4 v_dq4 &
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atom charge 5 v_dq5 &
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atom charge 6 v_dq6
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fix fFEP all ave/time 1 1 100 c_cFEP[1] c_cFEP[2] file bar10.lmp
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# compute cRDF all rdf 100 1 1
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# fix fRDF all ave/time 20 100 ${nsteps} c_cRDF file rdf.lammps mode vector
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# compute cMSD all msd
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# fix fMSD all ave/time 1 1 ${ndump} c_cMSD[1] c_cMSD[2] c_cMSD[3] c_cMSD[4] file msd.lammps
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dump dCONF all custom ${ndump} dump.lammpstrj id mol type element x y z ix iy iz
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dump_modify dCONF element C C H H O H H O
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# restart ${nrestart} restart.*.lmp
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run ${nsteps}
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write_restart restart.*.lmp
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write_data data.*.lmp
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File diff suppressed because it is too large
Load Diff
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@ -0,0 +1,22 @@
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# Time-averaged data for fix fFEP
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# TimeStep c_cFEP[1] c_cFEP[2]
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125000 0.00871763 0.985497
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250000 0.00705519 0.98825
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375000 0.00568771 0.99052
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500000 0.00429336 0.992842
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625000 0.00308675 0.994856
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750000 0.00169928 0.997181
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875000 0.000144366 0.999789
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1000000 -0.00112539 1.00193
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1125000 -0.0026842 1.00456
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1250000 -0.00474318 1.00805
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1375000 -0.00571651 1.0097
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1500000 -0.0073978 1.01256
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1625000 -0.00966334 1.01644
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1750000 -0.011584 1.01972
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1875000 -0.0148498 1.02535
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2000000 -0.0192874 1.03307
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2125000 -0.0257123 1.04433
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2250000 -0.035944 1.06249
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2375000 -0.046465 1.08144
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2500000 -0.0558595 1.09863
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@ -0,0 +1,142 @@
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# created by fftool
|
||||
|
||||
units real
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||||
boundary p p p
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||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
special_bonds lj/coul 0.0 0.0 0.5
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||||
|
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read_data data.0.lmp
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# read_restart restart.*.lmp
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# reset_timestep 0
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pair_style hybrid lj/cut/coul/long 10.0 10.0 &
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lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
|
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pair_modify tail no
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kspace_style pppm 1.0e-4
|
||||
|
||||
pair_coeff 1 1 none # C-CO C-CO
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||||
pair_coeff 1 2 none # C-CO C-D
|
||||
pair_coeff 1 3 none # C-CO H-D
|
||||
pair_coeff 1 4 none # C-CO H-H1
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||||
pair_coeff 1 5 none # C-CO OHD-
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||||
pair_coeff 1 6 none # C-CO HOD-
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||||
pair_coeff 1 7 lj/cut/coul/long 0.0000 1.0000 # C-CO Hw
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||||
pair_coeff 1 8 lj/cut/coul/long 0.1013 3.3286 # C-CO Ow
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||||
pair_coeff 2 2 none # C-D C-D
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pair_coeff 2 3 none # C-D H-D
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||||
pair_coeff 2 4 none # C-D H-H1
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||||
pair_coeff 2 5 none # C-D OHD-
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||||
pair_coeff 2 6 none # C-D HOD-
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||||
pair_coeff 2 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # C-D Hw
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||||
pair_coeff 2 8 lj/cut/coul/long/soft 0.1013 3.3286 1.0 # C-D Ow
|
||||
pair_coeff 3 3 none # H-D H-D
|
||||
pair_coeff 3 4 lj/cut/coul/long/soft 0.0300 2.5000 1.0 # H-D H-H1
|
||||
pair_coeff 3 5 none # H-D OHD-
|
||||
pair_coeff 3 6 none # H-D HOD-
|
||||
pair_coeff 3 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # H-D Hw
|
||||
pair_coeff 3 8 lj/cut/coul/long/soft 0.0683 2.8131 1.0 # H-D Ow
|
||||
pair_coeff 4 4 none # H-H1 H-H1
|
||||
pair_coeff 4 5 none # H-H1 OHD-
|
||||
pair_coeff 4 6 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # H-H1 HOD-
|
||||
pair_coeff 4 7 lj/cut/coul/long 0.0000 1.0000 # H-H1 Hw
|
||||
pair_coeff 4 8 lj/cut/coul/long 0.0683 2.8131 # H-H1 Ow
|
||||
pair_coeff 5 5 none # OHD- OHD-
|
||||
pair_coeff 5 6 none # OHD- HOD-
|
||||
pair_coeff 5 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # OHD- Hw
|
||||
pair_coeff 5 8 lj/cut/coul/long/soft 0.1625 3.1427 0.0 # OHD- Ow
|
||||
pair_coeff 6 6 none # HOD- HOD-
|
||||
pair_coeff 6 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # HOD- Hw
|
||||
pair_coeff 6 8 lj/cut/coul/long/soft 0.0000 1.7792 0.0 # HOD- Ow
|
||||
pair_coeff 7 7 lj/cut/coul/long 0.0000 1.0000 # Hw Hw
|
||||
pair_coeff 7 8 lj/cut/coul/long 0.0000 1.0000 # Hw Ow
|
||||
pair_coeff 8 8 lj/cut/coul/long 0.1554 3.1655 # Ow Ow
|
||||
|
||||
variable nsteps equal 2500000
|
||||
variable nprint equal ${nsteps}/500
|
||||
variable ndump equal ${nsteps}/100
|
||||
# variable nrestart equal ${nsteps}/10
|
||||
|
||||
variable temp equal 300.0
|
||||
variable press equal 1.0
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
timestep 2.0
|
||||
|
||||
velocity all create ${temp} 12345
|
||||
|
||||
thermo_style multi
|
||||
thermo ${nprint}
|
||||
|
||||
fix fSHAKE all shake 0.0001 20 ${nprint} b 2 4 5 a 6
|
||||
|
||||
fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 500
|
||||
|
||||
run 250000
|
||||
reset_timestep 0
|
||||
|
||||
|
||||
variable lambda equal ramp(0.0,1.0)
|
||||
variable minusl equal 1.0-v_lambda
|
||||
variable q1 equal 0.145*v_lambda-0.180*(1.0-v_lambda)
|
||||
variable q2 equal -0.180*(1.0-v_lambda)
|
||||
variable q3 equal 0.060*(1.0-v_lambda)
|
||||
variable q4 equal 0.040*v_lambda+0.060*(1.0-v_lambda)
|
||||
variable q5 equal -0.683*v_lambda
|
||||
variable q6 equal 0.418*v_lambda
|
||||
|
||||
fix fADAPT all adapt/fep 125000 &
|
||||
pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusl &
|
||||
pair lj/cut/coul/long/soft lambda 3 4 v_minusl &
|
||||
pair lj/cut/coul/long/soft lambda 4 6 v_lambda &
|
||||
pair lj/cut/coul/long/soft lambda 5*6 7*8 v_lambda &
|
||||
atom charge 1 v_q1 &
|
||||
atom charge 2 v_q2 &
|
||||
atom charge 3 v_q3 &
|
||||
atom charge 4 v_q4 &
|
||||
atom charge 5 v_q5 &
|
||||
atom charge 6 v_q6 &
|
||||
after yes
|
||||
|
||||
variable dlambda equal 0.002
|
||||
variable minusdl equal -0.002
|
||||
variable dq1 equal 0.145*v_dlambda+0.180*v_dlambda
|
||||
variable dq2 equal 0.180*v_dlambda
|
||||
variable dq3 equal -0.060*v_dlambda
|
||||
variable dq4 equal 0.040*v_dlambda-0.060*v_dlambda
|
||||
variable dq5 equal -0.683*v_dlambda
|
||||
variable dq6 equal 0.418*v_dlambda
|
||||
|
||||
compute cFEP all fep ${temp} &
|
||||
pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusdl &
|
||||
pair lj/cut/coul/long/soft lambda 3 4 v_minusdl &
|
||||
pair lj/cut/coul/long/soft lambda 4 6 v_dlambda &
|
||||
pair lj/cut/coul/long/soft lambda 5*6 7*8 v_dlambda &
|
||||
atom charge 1 v_dq1 &
|
||||
atom charge 2 v_dq2 &
|
||||
atom charge 3 v_dq3 &
|
||||
atom charge 4 v_dq4 &
|
||||
atom charge 5 v_dq5 &
|
||||
atom charge 6 v_dq6
|
||||
|
||||
fix fFEP all ave/time 25 4000 125000 c_cFEP[1] c_cFEP[2] file fdti01.lmp
|
||||
|
||||
# compute cRDF all rdf 100 1 1
|
||||
# fix fRDF all ave/time 20 100 ${nsteps} c_cRDF file rdf.lammps mode vector
|
||||
|
||||
compute cMSD all msd
|
||||
fix fMSD all ave/time 1 1 ${ndump} c_cMSD[1] c_cMSD[2] c_cMSD[3] c_cMSD[4] file msd.lammps
|
||||
|
||||
dump dCONF all custom ${ndump} dump.lammpstrj id mol type element x y z ix iy iz
|
||||
dump_modify dCONF element C C H H O H H O
|
||||
|
||||
# restart ${nrestart} restart.*.lmp
|
||||
|
||||
run ${nsteps}
|
||||
|
||||
write_restart restart.*.lmp
|
||||
write_data data.*.lmp
|
||||
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,22 @@
|
|||
# Time-averaged data for fix fFEP
|
||||
# TimeStep c_cFEP[1] c_cFEP[2]
|
||||
125000 0.0632017 0.899723
|
||||
250000 0.0561376 0.910429
|
||||
375000 0.0471384 0.924277
|
||||
500000 0.0349153 0.943416
|
||||
625000 0.0244399 0.960071
|
||||
750000 0.019451 0.968073
|
||||
875000 0.0134728 0.977767
|
||||
1000000 0.011723 0.980628
|
||||
1125000 0.00945656 0.984351
|
||||
1250000 0.00790634 0.986905
|
||||
1375000 0.00564311 0.990642
|
||||
1500000 0.00376572 0.993753
|
||||
1625000 0.00238483 0.996053
|
||||
1750000 0.00085649 0.9986
|
||||
1875000 -0.000515888 1.0009
|
||||
2000000 -0.00151569 1.00257
|
||||
2125000 -0.00325174 1.00549
|
||||
2250000 -0.00472612 1.00798
|
||||
2375000 -0.00578231 1.00976
|
||||
2500000 -0.00729864 1.01233
|
||||
|
|
@ -0,0 +1,142 @@
|
|||
# created by fftool
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
read_data data.1.lmp
|
||||
# read_restart restart.*.lmp
|
||||
# reset_timestep 0
|
||||
|
||||
pair_style hybrid lj/cut/coul/long 10.0 10.0 &
|
||||
lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
|
||||
pair_modify tail no
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
pair_coeff 1 1 none # CO-C CO-C
|
||||
pair_coeff 1 2 none # CO-C CD-
|
||||
pair_coeff 1 3 none # CO-C HD-
|
||||
pair_coeff 1 4 none # CO-C H1-H
|
||||
pair_coeff 1 5 none # CO-C OH-D
|
||||
pair_coeff 1 6 none # CO-C HO-D
|
||||
pair_coeff 1 7 lj/cut/coul/long 0.0000 1.0000 # CO-C Hw
|
||||
pair_coeff 1 8 lj/cut/coul/long 0.1013 3.3286 # CO-C Ow
|
||||
pair_coeff 2 2 none # CD- CD-
|
||||
pair_coeff 2 3 none # CD- HD-
|
||||
pair_coeff 2 4 none # CD- H1-H
|
||||
pair_coeff 2 5 none # CD- OH-D
|
||||
pair_coeff 2 6 none # CD- HO-D
|
||||
pair_coeff 2 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # CD- Hw
|
||||
pair_coeff 2 8 lj/cut/coul/long/soft 0.1013 3.3286 0.0 # CD- Ow
|
||||
pair_coeff 3 3 none # HD- HD-
|
||||
pair_coeff 3 4 lj/cut/coul/long/soft 0.0300 2.5000 0.0 # HD- H1-H
|
||||
pair_coeff 3 5 none # HD- OH-D
|
||||
pair_coeff 3 6 none # HD- HO-D
|
||||
pair_coeff 3 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # HD- Hw
|
||||
pair_coeff 3 8 lj/cut/coul/long/soft 0.0683 2.8131 0.0 # HD- Ow
|
||||
pair_coeff 4 4 none # H1-H H1-H
|
||||
pair_coeff 4 5 none # H1-H OH-D
|
||||
pair_coeff 4 6 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # H1-H HO-D
|
||||
pair_coeff 4 7 lj/cut/coul/long 0.0000 1.0000 # H1-H Hw
|
||||
pair_coeff 4 8 lj/cut/coul/long 0.0683 2.8131 # H1-H Ow
|
||||
pair_coeff 5 5 none # OH-D OH-D
|
||||
pair_coeff 5 6 none # OH-D HO-D
|
||||
pair_coeff 5 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # OH-D Hw
|
||||
pair_coeff 5 8 lj/cut/coul/long/soft 0.1625 3.1427 1.0 # OH-D Ow
|
||||
pair_coeff 6 6 none # HO-D HO-D
|
||||
pair_coeff 6 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # HO-D Hw
|
||||
pair_coeff 6 8 lj/cut/coul/long/soft 0.0000 1.7792 1.0 # HO-D Ow
|
||||
pair_coeff 7 7 lj/cut/coul/long 0.0000 1.0000 # Hw Hw
|
||||
pair_coeff 7 8 lj/cut/coul/long 0.0000 1.0000 # Hw Ow
|
||||
pair_coeff 8 8 lj/cut/coul/long 0.1554 3.1655 # Ow Ow
|
||||
|
||||
variable nsteps equal 2500000
|
||||
variable nprint equal ${nsteps}/500
|
||||
variable ndump equal ${nsteps}/100
|
||||
# variable nrestart equal ${nsteps}/10
|
||||
|
||||
variable temp equal 300.0
|
||||
variable press equal 1.0
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
timestep 2.0
|
||||
|
||||
velocity all create ${temp} 12345
|
||||
|
||||
thermo_style multi
|
||||
thermo ${nprint}
|
||||
|
||||
fix fSHAKE all shake 0.0001 20 ${nprint} b 2 4 5 a 6
|
||||
|
||||
fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 500
|
||||
|
||||
run 250000
|
||||
reset_timestep 0
|
||||
|
||||
|
||||
variable lambda equal ramp(1.0,0.0)
|
||||
variable minusl equal 1.0-v_lambda
|
||||
variable q1 equal 0.145*v_lambda-0.180*(1.0-v_lambda)
|
||||
variable q2 equal -0.180*(1.0-v_lambda)
|
||||
variable q3 equal 0.060*(1.0-v_lambda)
|
||||
variable q4 equal 0.040*v_lambda+0.060*(1.0-v_lambda)
|
||||
variable q5 equal -0.683*v_lambda
|
||||
variable q6 equal 0.418*v_lambda
|
||||
|
||||
fix fADAPT all adapt/fep 125000 &
|
||||
pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusl &
|
||||
pair lj/cut/coul/long/soft lambda 3 4 v_minusl &
|
||||
pair lj/cut/coul/long/soft lambda 4 6 v_lambda &
|
||||
pair lj/cut/coul/long/soft lambda 5*6 7*8 v_lambda &
|
||||
atom charge 1 v_q1 &
|
||||
atom charge 2 v_q2 &
|
||||
atom charge 3 v_q3 &
|
||||
atom charge 4 v_q4 &
|
||||
atom charge 5 v_q5 &
|
||||
atom charge 6 v_q6 &
|
||||
after yes
|
||||
|
||||
variable dlambda equal -0.002
|
||||
variable minusdl equal 0.002
|
||||
variable dq1 equal 0.145*v_dlambda+0.180*v_dlambda
|
||||
variable dq2 equal 0.180*v_dlambda
|
||||
variable dq3 equal -0.060*v_dlambda
|
||||
variable dq4 equal 0.040*v_dlambda-0.060*v_dlambda
|
||||
variable dq5 equal -0.683*v_dlambda
|
||||
variable dq6 equal 0.418*v_dlambda
|
||||
|
||||
compute cFEP all fep ${temp} &
|
||||
pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusdl &
|
||||
pair lj/cut/coul/long/soft lambda 3 4 v_minusdl &
|
||||
pair lj/cut/coul/long/soft lambda 4 6 v_dlambda &
|
||||
pair lj/cut/coul/long/soft lambda 5*6 7*8 v_dlambda &
|
||||
atom charge 1 v_dq1 &
|
||||
atom charge 2 v_dq2 &
|
||||
atom charge 3 v_dq3 &
|
||||
atom charge 4 v_dq4 &
|
||||
atom charge 5 v_dq5 &
|
||||
atom charge 6 v_dq6
|
||||
|
||||
fix fFEP all ave/time 25 4000 125000 c_cFEP[1] c_cFEP[2] file fdti10.lmp
|
||||
|
||||
# compute cRDF all rdf 100 1 1
|
||||
# fix fRDF all ave/time 20 100 ${nsteps} c_cRDF file rdf.lammps mode vector
|
||||
|
||||
compute cMSD all msd
|
||||
fix fMSD all ave/time 1 1 ${ndump} c_cMSD[1] c_cMSD[2] c_cMSD[3] c_cMSD[4] file msd.lammps
|
||||
|
||||
dump dCONF all custom ${ndump} dump.lammpstrj id mol type element x y z ix iy iz
|
||||
dump_modify dCONF element C C H H O H H O
|
||||
|
||||
# restart ${nrestart} restart.*.lmp
|
||||
|
||||
run ${nsteps}
|
||||
|
||||
write_restart restart.*.lmp
|
||||
write_data data.*.lmp
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,22 @@
|
|||
# Time-averaged data for fix fFEP
|
||||
# TimeStep c_cFEP[1] c_cFEP[2]
|
||||
125000 0.205889 0.714253
|
||||
250000 0.164934 0.765732
|
||||
375000 0.131935 0.809532
|
||||
500000 0.09771 0.859006
|
||||
625000 0.0688602 0.903005
|
||||
750000 0.0356141 0.958919
|
||||
875000 -0.00180317 1.02349
|
||||
1000000 -0.0317681 1.08115
|
||||
1125000 -0.0686221 1.15601
|
||||
1250000 -0.117495 1.2677
|
||||
1375000 -0.140627 1.31823
|
||||
1500000 -0.179791 1.41782
|
||||
1625000 -0.233651 1.57071
|
||||
1750000 -0.284345 1.71981
|
||||
1875000 -0.367527 2.01219
|
||||
2000000 -0.480496 2.54915
|
||||
2125000 -0.644218 3.47978
|
||||
2250000 -0.898797 5.57997
|
||||
2375000 -1.1516 8.56702
|
||||
2500000 -1.36364 12.2295
|
||||
|
|
@ -0,0 +1,143 @@
|
|||
# created by fftool
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
read_data data.0.lmp
|
||||
# read_restart restart.*.lmp
|
||||
# reset_timestep 0
|
||||
|
||||
pair_style hybrid lj/cut/coul/long 10.0 10.0 &
|
||||
lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
|
||||
pair_modify tail no
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
pair_coeff 1 1 none # C-CO C-CO
|
||||
pair_coeff 1 2 none # C-CO C-D
|
||||
pair_coeff 1 3 none # C-CO H-D
|
||||
pair_coeff 1 4 none # C-CO H-H1
|
||||
pair_coeff 1 5 none # C-CO OHD-
|
||||
pair_coeff 1 6 none # C-CO HOD-
|
||||
pair_coeff 1 7 lj/cut/coul/long 0.0000 1.0000 # C-CO Hw
|
||||
pair_coeff 1 8 lj/cut/coul/long 0.1013 3.3286 # C-CO Ow
|
||||
pair_coeff 2 2 none # C-D C-D
|
||||
pair_coeff 2 3 none # C-D H-D
|
||||
pair_coeff 2 4 none # C-D H-H1
|
||||
pair_coeff 2 5 none # C-D OHD-
|
||||
pair_coeff 2 6 none # C-D HOD-
|
||||
pair_coeff 2 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # C-D Hw
|
||||
pair_coeff 2 8 lj/cut/coul/long/soft 0.1013 3.3286 1.0 # C-D Ow
|
||||
pair_coeff 3 3 none # H-D H-D
|
||||
pair_coeff 3 4 lj/cut/coul/long/soft 0.0300 2.5000 1.0 # H-D H-H1
|
||||
pair_coeff 3 5 none # H-D OHD-
|
||||
pair_coeff 3 6 none # H-D HOD-
|
||||
pair_coeff 3 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # H-D Hw
|
||||
pair_coeff 3 8 lj/cut/coul/long/soft 0.0683 2.8131 1.0 # H-D Ow
|
||||
pair_coeff 4 4 none # H-H1 H-H1
|
||||
pair_coeff 4 5 none # H-H1 OHD-
|
||||
pair_coeff 4 6 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # H-H1 HOD-
|
||||
pair_coeff 4 7 lj/cut/coul/long 0.0000 1.0000 # H-H1 Hw
|
||||
pair_coeff 4 8 lj/cut/coul/long 0.0683 2.8131 # H-H1 Ow
|
||||
pair_coeff 5 5 none # OHD- OHD-
|
||||
pair_coeff 5 6 none # OHD- HOD-
|
||||
pair_coeff 5 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # OHD- Hw
|
||||
pair_coeff 5 8 lj/cut/coul/long/soft 0.1625 3.1427 0.0 # OHD- Ow
|
||||
pair_coeff 6 6 none # HOD- HOD-
|
||||
pair_coeff 6 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # HOD- Hw
|
||||
pair_coeff 6 8 lj/cut/coul/long/soft 0.0000 1.7792 0.0 # HOD- Ow
|
||||
pair_coeff 7 7 lj/cut/coul/long 0.0000 1.0000 # Hw Hw
|
||||
pair_coeff 7 8 lj/cut/coul/long 0.0000 1.0000 # Hw Ow
|
||||
pair_coeff 8 8 lj/cut/coul/long 0.1554 3.1655 # Ow Ow
|
||||
|
||||
variable nsteps equal 25000
|
||||
variable nprint equal ${nsteps}/500
|
||||
variable ndump equal ${nsteps}/100
|
||||
# variable nrestart equal ${nsteps}/10
|
||||
|
||||
variable temp equal 300.0
|
||||
variable press equal 1.0
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
timestep 2.0
|
||||
|
||||
# velocity all create ${temp} 12345
|
||||
|
||||
thermo_style multi
|
||||
thermo ${nprint}
|
||||
|
||||
fix fSHAKE all shake 0.0001 20 ${nprint} b 2 4 5 a 6
|
||||
|
||||
fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 500
|
||||
|
||||
run 10000
|
||||
reset_timestep 0
|
||||
write_restart init.restart
|
||||
|
||||
|
||||
variable lambda equal ramp(0.0,1.0)
|
||||
variable minusl equal 1.0-v_lambda
|
||||
variable q1 equal 0.145*v_lambda-0.180*(1.0-v_lambda)
|
||||
variable q2 equal -0.180*(1.0-v_lambda)
|
||||
variable q3 equal 0.060*(1.0-v_lambda)
|
||||
variable q4 equal 0.040*v_lambda+0.060*(1.0-v_lambda)
|
||||
variable q5 equal -0.683*v_lambda
|
||||
variable q6 equal 0.418*v_lambda
|
||||
|
||||
fix fADAPT all adapt/fep 125000 &
|
||||
pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusl &
|
||||
pair lj/cut/coul/long/soft lambda 3 4 v_minusl &
|
||||
pair lj/cut/coul/long/soft lambda 4 6 v_lambda &
|
||||
pair lj/cut/coul/long/soft lambda 5*6 7*8 v_lambda &
|
||||
atom charge 1 v_q1 &
|
||||
atom charge 2 v_q2 &
|
||||
atom charge 3 v_q3 &
|
||||
atom charge 4 v_q4 &
|
||||
atom charge 5 v_q5 &
|
||||
atom charge 6 v_q6 &
|
||||
after yes
|
||||
|
||||
variable dlambda equal 0.05
|
||||
variable minusdl equal -0.05
|
||||
variable dq1 equal 0.145*v_dlambda+0.180*v_dlambda
|
||||
variable dq2 equal 0.180*v_dlambda
|
||||
variable dq3 equal -0.060*v_dlambda
|
||||
variable dq4 equal 0.040*v_dlambda-0.060*v_dlambda
|
||||
variable dq5 equal -0.683*v_dlambda
|
||||
variable dq6 equal 0.418*v_dlambda
|
||||
|
||||
compute cFEP all fep ${temp} &
|
||||
pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusdl &
|
||||
pair lj/cut/coul/long/soft lambda 3 4 v_minusdl &
|
||||
pair lj/cut/coul/long/soft lambda 4 6 v_dlambda &
|
||||
pair lj/cut/coul/long/soft lambda 5*6 7*8 v_dlambda &
|
||||
atom charge 1 v_dq1 &
|
||||
atom charge 2 v_dq2 &
|
||||
atom charge 3 v_dq3 &
|
||||
atom charge 4 v_dq4 &
|
||||
atom charge 5 v_dq5 &
|
||||
atom charge 6 v_dq6
|
||||
|
||||
fix fFEP all ave/time 25 4000 125000 c_cFEP[1] c_cFEP[2] file fep01.lmp
|
||||
|
||||
# compute cRDF all rdf 100 1 1
|
||||
# fix fRDF all ave/time 20 100 ${nsteps} c_cRDF file rdf.lammps mode vector
|
||||
|
||||
compute cMSD all msd
|
||||
fix fMSD all ave/time 1 1 ${ndump} c_cMSD[1] c_cMSD[2] c_cMSD[3] c_cMSD[4] file msd.lammps
|
||||
|
||||
dump dCONF all custom ${ndump} dump.lammpstrj id mol type element x y z ix iy iz
|
||||
dump_modify dCONF element C C H H O H H O
|
||||
|
||||
# restart ${nrestart} restart.*.lmp
|
||||
|
||||
run ${nsteps}
|
||||
|
||||
write_restart restart.*.lmp
|
||||
write_data data.*.lmp
|
||||
|
|
@ -0,0 +1,142 @@
|
|||
# created by fftool
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
read_data data.0.lmp
|
||||
# read_restart restart.*.lmp
|
||||
# reset_timestep 0
|
||||
|
||||
pair_style hybrid lj/cut/coul/long 10.0 10.0 &
|
||||
lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
|
||||
pair_modify tail no
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
pair_coeff 1 1 none # C-CO C-CO
|
||||
pair_coeff 1 2 none # C-CO C-D
|
||||
pair_coeff 1 3 none # C-CO H-D
|
||||
pair_coeff 1 4 none # C-CO H-H1
|
||||
pair_coeff 1 5 none # C-CO OHD-
|
||||
pair_coeff 1 6 none # C-CO HOD-
|
||||
pair_coeff 1 7 lj/cut/coul/long 0.0000 1.0000 # C-CO Hw
|
||||
pair_coeff 1 8 lj/cut/coul/long 0.1013 3.3286 # C-CO Ow
|
||||
pair_coeff 2 2 none # C-D C-D
|
||||
pair_coeff 2 3 none # C-D H-D
|
||||
pair_coeff 2 4 none # C-D H-H1
|
||||
pair_coeff 2 5 none # C-D OHD-
|
||||
pair_coeff 2 6 none # C-D HOD-
|
||||
pair_coeff 2 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # C-D Hw
|
||||
pair_coeff 2 8 lj/cut/coul/long/soft 0.1013 3.3286 1.0 # C-D Ow
|
||||
pair_coeff 3 3 none # H-D H-D
|
||||
pair_coeff 3 4 lj/cut/coul/long/soft 0.0300 2.5000 1.0 # H-D H-H1
|
||||
pair_coeff 3 5 none # H-D OHD-
|
||||
pair_coeff 3 6 none # H-D HOD-
|
||||
pair_coeff 3 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # H-D Hw
|
||||
pair_coeff 3 8 lj/cut/coul/long/soft 0.0683 2.8131 1.0 # H-D Ow
|
||||
pair_coeff 4 4 none # H-H1 H-H1
|
||||
pair_coeff 4 5 none # H-H1 OHD-
|
||||
pair_coeff 4 6 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # H-H1 HOD-
|
||||
pair_coeff 4 7 lj/cut/coul/long 0.0000 1.0000 # H-H1 Hw
|
||||
pair_coeff 4 8 lj/cut/coul/long 0.0683 2.8131 # H-H1 Ow
|
||||
pair_coeff 5 5 none # OHD- OHD-
|
||||
pair_coeff 5 6 none # OHD- HOD-
|
||||
pair_coeff 5 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # OHD- Hw
|
||||
pair_coeff 5 8 lj/cut/coul/long/soft 0.1625 3.1427 0.0 # OHD- Ow
|
||||
pair_coeff 6 6 none # HOD- HOD-
|
||||
pair_coeff 6 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # HOD- Hw
|
||||
pair_coeff 6 8 lj/cut/coul/long/soft 0.0000 1.7792 0.0 # HOD- Ow
|
||||
pair_coeff 7 7 lj/cut/coul/long 0.0000 1.0000 # Hw Hw
|
||||
pair_coeff 7 8 lj/cut/coul/long 0.0000 1.0000 # Hw Ow
|
||||
pair_coeff 8 8 lj/cut/coul/long 0.1554 3.1655 # Ow Ow
|
||||
|
||||
variable nsteps equal 2500000
|
||||
variable nprint equal ${nsteps}/500
|
||||
variable ndump equal ${nsteps}/100
|
||||
# variable nrestart equal ${nsteps}/10
|
||||
|
||||
variable temp equal 300.0
|
||||
variable press equal 1.0
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
timestep 2.0
|
||||
|
||||
velocity all create ${temp} 12345
|
||||
|
||||
thermo_style multi
|
||||
thermo ${nprint}
|
||||
|
||||
fix fSHAKE all shake 0.0001 20 ${nprint} b 2 4 5 a 6
|
||||
|
||||
fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 500
|
||||
|
||||
run 250000
|
||||
reset_timestep 0
|
||||
|
||||
|
||||
variable lambda equal ramp(0.0,1.0)
|
||||
variable minusl equal 1.0-v_lambda
|
||||
variable q1 equal 0.145*v_lambda-0.180*(1.0-v_lambda)
|
||||
variable q2 equal -0.180*(1.0-v_lambda)
|
||||
variable q3 equal 0.060*(1.0-v_lambda)
|
||||
variable q4 equal 0.040*v_lambda+0.060*(1.0-v_lambda)
|
||||
variable q5 equal -0.683*v_lambda
|
||||
variable q6 equal 0.418*v_lambda
|
||||
|
||||
fix fADAPT all adapt/fep 125000 &
|
||||
pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusl &
|
||||
pair lj/cut/coul/long/soft lambda 3 4 v_minusl &
|
||||
pair lj/cut/coul/long/soft lambda 4 6 v_lambda &
|
||||
pair lj/cut/coul/long/soft lambda 5*6 7*8 v_lambda &
|
||||
atom charge 1 v_q1 &
|
||||
atom charge 2 v_q2 &
|
||||
atom charge 3 v_q3 &
|
||||
atom charge 4 v_q4 &
|
||||
atom charge 5 v_q5 &
|
||||
atom charge 6 v_q6 &
|
||||
after yes
|
||||
|
||||
variable dlambda equal 0.05
|
||||
variable minusdl equal -0.05
|
||||
variable dq1 equal 0.145*v_dlambda+0.180*v_dlambda
|
||||
variable dq2 equal 0.180*v_dlambda
|
||||
variable dq3 equal -0.060*v_dlambda
|
||||
variable dq4 equal 0.040*v_dlambda-0.060*v_dlambda
|
||||
variable dq5 equal -0.683*v_dlambda
|
||||
variable dq6 equal 0.418*v_dlambda
|
||||
|
||||
compute cFEP all fep ${temp} &
|
||||
pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusdl &
|
||||
pair lj/cut/coul/long/soft lambda 3 4 v_minusdl &
|
||||
pair lj/cut/coul/long/soft lambda 4 6 v_dlambda &
|
||||
pair lj/cut/coul/long/soft lambda 5*6 7*8 v_dlambda &
|
||||
atom charge 1 v_dq1 &
|
||||
atom charge 2 v_dq2 &
|
||||
atom charge 3 v_dq3 &
|
||||
atom charge 4 v_dq4 &
|
||||
atom charge 5 v_dq5 &
|
||||
atom charge 6 v_dq6
|
||||
|
||||
fix fFEP all ave/time 25 4000 125000 c_cFEP[1] c_cFEP[2] file fep01.lmp
|
||||
|
||||
# compute cRDF all rdf 100 1 1
|
||||
# fix fRDF all ave/time 20 100 ${nsteps} c_cRDF file rdf.lammps mode vector
|
||||
|
||||
compute cMSD all msd
|
||||
fix fMSD all ave/time 1 1 ${ndump} c_cMSD[1] c_cMSD[2] c_cMSD[3] c_cMSD[4] file msd.lammps
|
||||
|
||||
dump dCONF all custom ${ndump} dump.lammpstrj id mol type element x y z ix iy iz
|
||||
dump_modify dCONF element C C H H O H H O
|
||||
|
||||
# restart ${nrestart} restart.*.lmp
|
||||
|
||||
run ${nsteps}
|
||||
|
||||
write_restart restart.*.lmp
|
||||
write_data data.*.lmp
|
||||
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,285 @@
|
|||
LAMMPS (18 Apr 2014-ICMS)
|
||||
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# created by fftool
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
read_data data.0.lmp
|
||||
orthogonal box = (-13.4438 -13.4438 -13.4438) to (13.4438 13.4438 13.4438)
|
||||
2 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
1090 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
scanning angles ...
|
||||
10 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
12 = max dihedrals/atom
|
||||
reading bonds ...
|
||||
729 bonds
|
||||
reading angles ...
|
||||
377 angles
|
||||
reading dihedrals ...
|
||||
16 dihedrals
|
||||
5 = max # of 1-2 neighbors
|
||||
4 = max # of 1-3 neighbors
|
||||
8 = max # of 1-4 neighbors
|
||||
9 = max # of special neighbors
|
||||
# read_restart restart.*.lmp
|
||||
# reset_timestep 0
|
||||
|
||||
pair_style hybrid lj/cut/coul/long 10.0 10.0 lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
|
||||
pair_modify tail no
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
pair_coeff 1 1 none # C-CO C-CO
|
||||
pair_coeff 1 2 none # C-CO C-D
|
||||
pair_coeff 1 3 none # C-CO H-D
|
||||
pair_coeff 1 4 none # C-CO H-H1
|
||||
pair_coeff 1 5 none # C-CO OHD-
|
||||
pair_coeff 1 6 none # C-CO HOD-
|
||||
pair_coeff 1 7 lj/cut/coul/long 0.0000 1.0000 # C-CO Hw
|
||||
pair_coeff 1 8 lj/cut/coul/long 0.1013 3.3286 # C-CO Ow
|
||||
pair_coeff 2 2 none # C-D C-D
|
||||
pair_coeff 2 3 none # C-D H-D
|
||||
pair_coeff 2 4 none # C-D H-H1
|
||||
pair_coeff 2 5 none # C-D OHD-
|
||||
pair_coeff 2 6 none # C-D HOD-
|
||||
pair_coeff 2 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # C-D Hw
|
||||
pair_coeff 2 8 lj/cut/coul/long/soft 0.1013 3.3286 1.0 # C-D Ow
|
||||
pair_coeff 3 3 none # H-D H-D
|
||||
pair_coeff 3 4 lj/cut/coul/long/soft 0.0300 2.5000 1.0 # H-D H-H1
|
||||
pair_coeff 3 5 none # H-D OHD-
|
||||
pair_coeff 3 6 none # H-D HOD-
|
||||
pair_coeff 3 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # H-D Hw
|
||||
pair_coeff 3 8 lj/cut/coul/long/soft 0.0683 2.8131 1.0 # H-D Ow
|
||||
pair_coeff 4 4 none # H-H1 H-H1
|
||||
pair_coeff 4 5 none # H-H1 OHD-
|
||||
pair_coeff 4 6 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # H-H1 HOD-
|
||||
pair_coeff 4 7 lj/cut/coul/long 0.0000 1.0000 # H-H1 Hw
|
||||
pair_coeff 4 8 lj/cut/coul/long 0.0683 2.8131 # H-H1 Ow
|
||||
pair_coeff 5 5 none # OHD- OHD-
|
||||
pair_coeff 5 6 none # OHD- HOD-
|
||||
pair_coeff 5 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # OHD- Hw
|
||||
pair_coeff 5 8 lj/cut/coul/long/soft 0.1625 3.1427 0.0 # OHD- Ow
|
||||
pair_coeff 6 6 none # HOD- HOD-
|
||||
pair_coeff 6 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # HOD- Hw
|
||||
pair_coeff 6 8 lj/cut/coul/long/soft 0.0000 1.7792 0.0 # HOD- Ow
|
||||
pair_coeff 7 7 lj/cut/coul/long 0.0000 1.0000 # Hw Hw
|
||||
pair_coeff 7 8 lj/cut/coul/long 0.0000 1.0000 # Hw Ow
|
||||
pair_coeff 8 8 lj/cut/coul/long 0.1554 3.1655 # Ow Ow
|
||||
|
||||
variable nsteps equal 2500000
|
||||
variable nprint equal ${nsteps}/500
|
||||
variable nprint equal 2500000/500
|
||||
variable ndump equal ${nsteps}/100
|
||||
variable ndump equal 2500000/100
|
||||
# variable nrestart equal ${nsteps}/10
|
||||
|
||||
variable temp equal 300.0
|
||||
variable press equal 1.0
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
timestep 2.0
|
||||
|
||||
# velocity all create ${temp} 12345
|
||||
|
||||
thermo_style multi
|
||||
thermo ${nprint}
|
||||
thermo 5000
|
||||
|
||||
fix fSHAKE all shake 0.0001 20 ${nprint} b 2 4 5 a 6
|
||||
fix fSHAKE all shake 0.0001 20 5000 b 2 4 5 a 6
|
||||
1 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
2 = # of size 4 clusters
|
||||
360 = # of frozen angles
|
||||
|
||||
fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 500
|
||||
fix fNPT all npt temp 300 ${temp} 100 iso ${press} ${press} 500
|
||||
fix fNPT all npt temp 300 300 100 iso ${press} ${press} 500
|
||||
fix fNPT all npt temp 300 300 100 iso 1 ${press} 500
|
||||
fix fNPT all npt temp 300 300 100 iso 1 1 500
|
||||
|
||||
run 250000
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.270213
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0169033
|
||||
estimated relative force accuracy = 5.09037e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 2744 512
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
2 1.09 4.99625e-06
|
||||
4 0.945001 0
|
||||
5 1 1.58341e-05
|
||||
6 109.47 0.0012593
|
||||
Memory usage per processor = 8.38576 Mbytes
|
||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||
TotEng = -236.7999 KinEng = 0.0000 Temp = 0.0000
|
||||
PotEng = -236.7999 E_bond = 0.0000 E_angle = 0.3094
|
||||
E_dihed = 0.0001 E_impro = 0.0000 E_vdwl = -192.9285
|
||||
E_coul = 19402.7702 E_long = -19446.9511 Press = 406.6448
|
||||
Volume = 19438.0383
|
||||
SHAKE stats (type/ave/delta) on step 5000
|
||||
2 1.09006 8.6791e-07
|
||||
4 0.945054 0
|
||||
5 1.00006 3.8639e-06
|
||||
6 109.47 0.000376049
|
||||
---------------- Step 5000 ----- CPU = 16.4963 (sec) ----------------
|
||||
TotEng = -3314.5713 KinEng = 650.7183 Temp = 300.4163
|
||||
PotEng = -3965.2896 E_bond = 0.0875 E_angle = 1.4729
|
||||
E_dihed = 0.4749 E_impro = 0.0000 E_vdwl = 774.1508
|
||||
E_coul = 14908.3382 E_long = -19649.8139 Press = 358.7253
|
||||
Volume = 10987.1076
|
||||
SHAKE stats (type/ave/delta) on step 10000
|
||||
2 1.08998 2.43077e-07
|
||||
4 0.944985 0
|
||||
5 0.999985 4.10972e-06
|
||||
6 109.47 0.000514527
|
||||
---------------- Step 10000 ----- CPU = 34.0488 (sec) ----------------
|
||||
TotEng = -3279.4541 KinEng = 689.4215 Temp = 318.2843
|
||||
PotEng = -3968.8755 E_bond = 0.2040 E_angle = 1.8441
|
||||
E_dihed = 0.1574 E_impro = 0.0000 E_vdwl = 703.3180
|
||||
E_coul = 14976.4466 E_long = -19650.8457 Press = -983.5171
|
||||
Volume = 10927.3524
|
||||
SHAKE stats (type/ave/delta) on step 15000
|
||||
2 1.09002 1.0199e-06
|
||||
4 0.945017 0
|
||||
5 1.00002 5.08944e-06
|
||||
6 109.47 0.00042735
|
||||
---------------- Step 15000 ----- CPU = 53.1541 (sec) ----------------
|
||||
TotEng = -3368.2566 KinEng = 686.6827 Temp = 317.0199
|
||||
PotEng = -4054.9393 E_bond = 0.4514 E_angle = 1.5194
|
||||
E_dihed = 2.4125 E_impro = 0.0000 E_vdwl = 709.7507
|
||||
E_coul = 14880.7025 E_long = -19649.7759 Press = -1277.1945
|
||||
Volume = 10817.2760
|
||||
SHAKE stats (type/ave/delta) on step 20000
|
||||
2 1.09005 3.84509e-06
|
||||
4 0.945044 0
|
||||
5 1.00005 1.15463e-05
|
||||
6 109.47 0.000893174
|
||||
---------------- Step 20000 ----- CPU = 67.0658 (sec) ----------------
|
||||
TotEng = -3401.0672 KinEng = 639.1818 Temp = 295.0902
|
||||
PotEng = -4040.2490 E_bond = 0.8254 E_angle = 4.2422
|
||||
E_dihed = 0.6223 E_impro = 0.0000 E_vdwl = 777.7799
|
||||
E_coul = 14826.3237 E_long = -19650.0425 Press = -268.5153
|
||||
Volume = 10911.3140
|
||||
SHAKE stats (type/ave/delta) on step 25000
|
||||
2 1.09 3.16085e-06
|
||||
4 0.945002 0
|
||||
5 1 6.82105e-06
|
||||
6 109.47 0.000683982
|
||||
---------------- Step 25000 ----- CPU = 83.1242 (sec) ----------------
|
||||
TotEng = -3331.9648 KinEng = 658.5638 Temp = 304.0383
|
||||
PotEng = -3990.5287 E_bond = 0.0504 E_angle = 4.8757
|
||||
E_dihed = 0.9548 E_impro = 0.0000 E_vdwl = 742.1312
|
||||
E_coul = 14907.2989 E_long = -19645.8396 Press = -803.8894
|
||||
Volume = 11243.5807
|
||||
SHAKE stats (type/ave/delta) on step 30000
|
||||
2 1.08995 5.90921e-08
|
||||
4 0.944954 0
|
||||
5 0.999952 5.01043e-06
|
||||
6 109.47 0.000369665
|
||||
---------------- Step 30000 ----- CPU = 96.1911 (sec) ----------------
|
||||
TotEng = -3321.5197 KinEng = 681.8132 Temp = 314.7718
|
||||
PotEng = -4003.3328 E_bond = 0.5162 E_angle = 6.2281
|
||||
E_dihed = 1.2145 E_impro = 0.0000 E_vdwl = 767.4719
|
||||
E_coul = 14871.6899 E_long = -19650.4535 Press = 63.7724
|
||||
Volume = 10913.5775
|
||||
SHAKE stats (type/ave/delta) on step 35000
|
||||
2 1.08996 3.93868e-07
|
||||
4 0.944963 0
|
||||
5 0.999961 4.01003e-06
|
||||
6 109.47 0.000492251
|
||||
---------------- Step 35000 ----- CPU = 111.1547 (sec) ----------------
|
||||
TotEng = -3376.3100 KinEng = 652.5134 Temp = 301.2450
|
||||
PotEng = -4028.8234 E_bond = 0.6940 E_angle = 3.8874
|
||||
E_dihed = 0.6796 E_impro = 0.0000 E_vdwl = 811.7936
|
||||
E_coul = 14803.9468 E_long = -19649.8247 Press = 957.3673
|
||||
Volume = 10810.8812
|
||||
SHAKE stats (type/ave/delta) on step 40000
|
||||
2 1.08993 1.84911e-06
|
||||
4 0.944937 0
|
||||
5 0.999934 4.48159e-06
|
||||
6 109.47 0.000423379
|
||||
---------------- Step 40000 ----- CPU = 127.8336 (sec) ----------------
|
||||
TotEng = -3342.5048 KinEng = 641.0827 Temp = 295.9678
|
||||
PotEng = -3983.5875 E_bond = 1.4592 E_angle = 3.3579
|
||||
E_dihed = 0.1250 E_impro = 0.0000 E_vdwl = 714.5090
|
||||
E_coul = 14945.5914 E_long = -19648.6299 Press = -1146.3509
|
||||
Volume = 10993.6945
|
||||
SHAKE stats (type/ave/delta) on step 45000
|
||||
2 1.09004 2.52413e-06
|
||||
4 0.945038 0
|
||||
5 1.00004 7.30752e-06
|
||||
6 109.47 0.000660905
|
||||
---------------- Step 45000 ----- CPU = 141.7030 (sec) ----------------
|
||||
TotEng = -3368.5223 KinEng = 640.7082 Temp = 295.7949
|
||||
PotEng = -4009.2305 E_bond = 0.0226 E_angle = 2.7492
|
||||
E_dihed = 0.8929 E_impro = 0.0000 E_vdwl = 820.3025
|
||||
E_coul = 14817.6347 E_long = -19650.8325 Press = 388.8981
|
||||
Volume = 11292.9397
|
||||
SHAKE stats (type/ave/delta) on step 50000
|
||||
2 1.09006 2.89749e-06
|
||||
4 0.945051 0
|
||||
5 1.00006 6.08927e-06
|
||||
6 109.47 0.000779845
|
||||
---------------- Step 50000 ----- CPU = 156.2936 (sec) ----------------
|
||||
TotEng = -3253.6028 KinEng = 683.0893 Temp = 315.3610
|
||||
PotEng = -3936.6921 E_bond = 0.4303 E_angle = 5.1773
|
||||
E_dihed = 1.1538 E_impro = 0.0000 E_vdwl = 722.3282
|
||||
E_coul = 14982.9162 E_long = -19648.6979 Press = -338.7238
|
||||
Volume = 11230.1507
|
||||
SHAKE stats (type/ave/delta) on step 55000
|
||||
2 1.09007 9.95472e-07
|
||||
4 0.945062 0
|
||||
5 1.00007 3.93786e-06
|
||||
6 109.47 0.000436645
|
||||
---------------- Step 55000 ----- CPU = 176.2674 (sec) ----------------
|
||||
TotEng = -3332.0820 KinEng = 662.9270 Temp = 306.0527
|
||||
PotEng = -3995.0090 E_bond = 0.8395 E_angle = 1.9527
|
||||
E_dihed = 1.0770 E_impro = 0.0000 E_vdwl = 750.6359
|
||||
E_coul = 14899.3802 E_long = -19648.8943 Press = -498.7755
|
||||
Volume = 11082.6763
|
||||
SHAKE stats (type/ave/delta) on step 60000
|
||||
2 1.09006 7.79087e-08
|
||||
4 0.945052 1.22125e-15
|
||||
5 1.00006 3.87615e-06
|
||||
6 109.47 0.000355506
|
||||
---------------- Step 60000 ----- CPU = 193.3379 (sec) ----------------
|
||||
TotEng = -3296.5834 KinEng = 679.6746 Temp = 313.7845
|
||||
PotEng = -3976.2580 E_bond = 2.4610 E_angle = 2.9231
|
||||
E_dihed = 0.8719 E_impro = 0.0000 E_vdwl = 803.1348
|
||||
E_coul = 14863.3163 E_long = -19648.9651 Press = 1009.2429
|
||||
Volume = 11125.1736
|
||||
SHAKE stats (type/ave/delta) on step 65000
|
||||
2 1.09003 1.05995e-06
|
||||
4 0.945023 1.22125e-15
|
||||
5 1.00003 4.3471e-06
|
||||
6 109.47 0.000511365
|
||||
---------------- Step 65000 ----- CPU = 210.3194 (sec) ----------------
|
||||
TotEng = -3322.0496 KinEng = 666.5091 Temp = 307.7064
|
||||
PotEng = -3988.5587 E_bond = 0.8728 E_angle = 5.7476
|
||||
E_dihed = 0.9783 E_impro = 0.0000 E_vdwl = 743.8165
|
||||
E_coul = 14910.0426 E_long = -19650.0166 Press = -421.7167
|
||||
Volume = 10902.5998
|
||||
SHAKE stats (type/ave/delta) on step 70000
|
||||
2 1.0901 1.09831e-06
|
||||
4 0.94509 0
|
||||
5 1.0001 3.59309e-06
|
||||
6 109.47 0.000361318
|
||||
---------------- Step 70000 ----- CPU = 228.7878 (sec) ----------------
|
||||
TotEng = -3395.7912 KinEng = 667.4514 Temp = 308.1414
|
||||
PotEng = -4063.2426 E_bond = 0.6965 E_angle = 5.1350
|
||||
E_dihed
|
||||
|
|
@ -0,0 +1,287 @@
|
|||
LAMMPS (18 Apr 2014-ICMS)
|
||||
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
package omp *
|
||||
using multi-threaded neighbor list subroutines
|
||||
prefer double precision OpenMP force kernels
|
||||
# created by fftool
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
read_data data.0.lmp
|
||||
orthogonal box = (-13.4438 -13.4438 -13.4438) to (13.4438 13.4438 13.4438)
|
||||
2 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
1090 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
scanning angles ...
|
||||
10 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
12 = max dihedrals/atom
|
||||
reading bonds ...
|
||||
729 bonds
|
||||
reading angles ...
|
||||
377 angles
|
||||
reading dihedrals ...
|
||||
16 dihedrals
|
||||
5 = max # of 1-2 neighbors
|
||||
4 = max # of 1-3 neighbors
|
||||
8 = max # of 1-4 neighbors
|
||||
9 = max # of special neighbors
|
||||
# read_restart restart.*.lmp
|
||||
# reset_timestep 0
|
||||
|
||||
pair_style hybrid lj/cut/coul/long 10.0 10.0 lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
|
||||
pair_modify tail no
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
pair_coeff 1 1 none # C-CO C-CO
|
||||
pair_coeff 1 2 none # C-CO C-D
|
||||
pair_coeff 1 3 none # C-CO H-D
|
||||
pair_coeff 1 4 none # C-CO H-H1
|
||||
pair_coeff 1 5 none # C-CO OHD-
|
||||
pair_coeff 1 6 none # C-CO HOD-
|
||||
pair_coeff 1 7 lj/cut/coul/long 0.0000 1.0000 # C-CO Hw
|
||||
pair_coeff 1 8 lj/cut/coul/long 0.1013 3.3286 # C-CO Ow
|
||||
pair_coeff 2 2 none # C-D C-D
|
||||
pair_coeff 2 3 none # C-D H-D
|
||||
pair_coeff 2 4 none # C-D H-H1
|
||||
pair_coeff 2 5 none # C-D OHD-
|
||||
pair_coeff 2 6 none # C-D HOD-
|
||||
pair_coeff 2 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # C-D Hw
|
||||
pair_coeff 2 8 lj/cut/coul/long/soft 0.1013 3.3286 1.0 # C-D Ow
|
||||
pair_coeff 3 3 none # H-D H-D
|
||||
pair_coeff 3 4 lj/cut/coul/long/soft 0.0300 2.5000 1.0 # H-D H-H1
|
||||
pair_coeff 3 5 none # H-D OHD-
|
||||
pair_coeff 3 6 none # H-D HOD-
|
||||
pair_coeff 3 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # H-D Hw
|
||||
pair_coeff 3 8 lj/cut/coul/long/soft 0.0683 2.8131 1.0 # H-D Ow
|
||||
pair_coeff 4 4 none # H-H1 H-H1
|
||||
pair_coeff 4 5 none # H-H1 OHD-
|
||||
pair_coeff 4 6 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # H-H1 HOD-
|
||||
pair_coeff 4 7 lj/cut/coul/long 0.0000 1.0000 # H-H1 Hw
|
||||
pair_coeff 4 8 lj/cut/coul/long 0.0683 2.8131 # H-H1 Ow
|
||||
pair_coeff 5 5 none # OHD- OHD-
|
||||
pair_coeff 5 6 none # OHD- HOD-
|
||||
pair_coeff 5 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # OHD- Hw
|
||||
pair_coeff 5 8 lj/cut/coul/long/soft 0.1625 3.1427 0.0 # OHD- Ow
|
||||
pair_coeff 6 6 none # HOD- HOD-
|
||||
pair_coeff 6 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # HOD- Hw
|
||||
pair_coeff 6 8 lj/cut/coul/long/soft 0.0000 1.7792 0.0 # HOD- Ow
|
||||
pair_coeff 7 7 lj/cut/coul/long 0.0000 1.0000 # Hw Hw
|
||||
pair_coeff 7 8 lj/cut/coul/long 0.0000 1.0000 # Hw Ow
|
||||
pair_coeff 8 8 lj/cut/coul/long 0.1554 3.1655 # Ow Ow
|
||||
|
||||
variable nsteps equal 2500000
|
||||
variable nprint equal ${nsteps}/500
|
||||
variable nprint equal 2500000/500
|
||||
variable ndump equal ${nsteps}/100
|
||||
variable ndump equal 2500000/100
|
||||
# variable nrestart equal ${nsteps}/10
|
||||
|
||||
variable temp equal 300.0
|
||||
variable press equal 1.0
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
timestep 2.0
|
||||
|
||||
# velocity all create ${temp} 12345
|
||||
|
||||
thermo_style multi
|
||||
thermo ${nprint}
|
||||
thermo 5000
|
||||
|
||||
fix fSHAKE all shake 0.0001 20 ${nprint} b 2 4 5 a 6
|
||||
fix fSHAKE all shake 0.0001 20 5000 b 2 4 5 a 6
|
||||
1 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
2 = # of size 4 clusters
|
||||
360 = # of frozen angles
|
||||
|
||||
fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 500
|
||||
fix fNPT all npt temp 300 ${temp} 100 iso ${press} ${press} 500
|
||||
fix fNPT all npt temp 300 300 100 iso ${press} ${press} 500
|
||||
fix fNPT all npt temp 300 300 100 iso 1 ${press} 500
|
||||
fix fNPT all npt temp 300 300 100 iso 1 1 500
|
||||
|
||||
run 250000
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.270213
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0169033
|
||||
estimated relative force accuracy = 5.09037e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 2744 512
|
||||
Hybrid pair style last /omp style lj/cut/coul/long/soft
|
||||
Last active /omp style is kspace_style pppm/omp
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
2 1.09 4.99625e-06
|
||||
4 0.945001 0
|
||||
5 1 1.58341e-05
|
||||
6 109.47 0.0012593
|
||||
Memory usage per processor = 8.38667 Mbytes
|
||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||
TotEng = -236.7999 KinEng = 0.0000 Temp = 0.0000
|
||||
PotEng = -236.7999 E_bond = 0.0000 E_angle = 0.3094
|
||||
E_dihed = 0.0001 E_impro = 0.0000 E_vdwl = -192.9285
|
||||
E_coul = 19402.7702 E_long = -19446.9511 Press = 406.6448
|
||||
Volume = 19438.0383
|
||||
SHAKE stats (type/ave/delta) on step 5000
|
||||
2 1.09009 2.87398e-07
|
||||
4 0.945079 0
|
||||
5 1.00008 3.9811e-06
|
||||
6 109.47 0.000369321
|
||||
---------------- Step 5000 ----- CPU = 11.8253 (sec) ----------------
|
||||
TotEng = -3307.2904 KinEng = 658.6061 Temp = 304.0578
|
||||
PotEng = -3965.8965 E_bond = 0.0083 E_angle = 0.6669
|
||||
E_dihed = 0.2569 E_impro = 0.0000 E_vdwl = 734.5556
|
||||
E_coul = 14945.5504 E_long = -19646.9346 Press = -401.3652
|
||||
Volume = 10990.0279
|
||||
SHAKE stats (type/ave/delta) on step 10000
|
||||
2 1.08991 8.10164e-07
|
||||
4 0.944925 0
|
||||
5 0.999922 7.76553e-06
|
||||
6 109.47 0.000694232
|
||||
---------------- Step 10000 ----- CPU = 23.7032 (sec) ----------------
|
||||
TotEng = -3381.5340 KinEng = 646.2577 Temp = 298.3570
|
||||
PotEng = -4027.7917 E_bond = 0.2113 E_angle = 1.2103
|
||||
E_dihed = 0.8831 E_impro = 0.0000 E_vdwl = 807.4931
|
||||
E_coul = 14812.7871 E_long = -19650.3766 Press = 1168.7845
|
||||
Volume = 10591.5096
|
||||
SHAKE stats (type/ave/delta) on step 15000
|
||||
2 1.08988 6.96695e-07
|
||||
4 0.944894 0
|
||||
5 0.999889 7.87681e-06
|
||||
6 109.47 0.000849755
|
||||
---------------- Step 15000 ----- CPU = 37.0159 (sec) ----------------
|
||||
TotEng = -3391.4919 KinEng = 640.6926 Temp = 295.7878
|
||||
PotEng = -4032.1845 E_bond = 0.3271 E_angle = 2.4027
|
||||
E_dihed = 0.2102 E_impro = 0.0000 E_vdwl = 833.3641
|
||||
E_coul = 14781.8806 E_long = -19650.3692 Press = 1246.1602
|
||||
Volume = 10806.8631
|
||||
SHAKE stats (type/ave/delta) on step 20000
|
||||
2 1.09009 5.35061e-07
|
||||
4 0.945076 0
|
||||
5 1.00008 5.8947e-06
|
||||
6 109.47 0.000481652
|
||||
---------------- Step 20000 ----- CPU = 49.5427 (sec) ----------------
|
||||
TotEng = -3340.9663 KinEng = 649.0129 Temp = 299.6290
|
||||
PotEng = -3989.9791 E_bond = 0.2338 E_angle = 1.4422
|
||||
E_dihed = 0.7066 E_impro = 0.0000 E_vdwl = 823.4408
|
||||
E_coul = 14835.4457 E_long = -19651.2482 Press = 1369.0812
|
||||
Volume = 10984.3808
|
||||
SHAKE stats (type/ave/delta) on step 25000
|
||||
2 1.09003 1.29003e-06
|
||||
4 0.945026 0
|
||||
5 1.00003 5.08541e-06
|
||||
6 109.47 0.000543653
|
||||
---------------- Step 25000 ----- CPU = 61.5352 (sec) ----------------
|
||||
TotEng = -3350.1301 KinEng = 628.6694 Temp = 290.2370
|
||||
PotEng = -3978.7994 E_bond = 0.5250 E_angle = 3.3362
|
||||
E_dihed = 1.1997 E_impro = 0.0000 E_vdwl = 753.6460
|
||||
E_coul = 14908.8825 E_long = -19646.3890 Press = -107.3383
|
||||
Volume = 10858.4423
|
||||
SHAKE stats (type/ave/delta) on step 30000
|
||||
2 1.09012 2.15723e-06
|
||||
4 0.945104 0
|
||||
5 1.00011 7.30223e-06
|
||||
6 109.47 0.000722195
|
||||
---------------- Step 30000 ----- CPU = 75.1590 (sec) ----------------
|
||||
TotEng = -3291.1533 KinEng = 662.9659 Temp = 306.0706
|
||||
PotEng = -3954.1192 E_bond = 0.0386 E_angle = 3.4541
|
||||
E_dihed = 0.3158 E_impro = 0.0000 E_vdwl = 745.0479
|
||||
E_coul = 14947.2099 E_long = -19650.1856 Press = -296.2930
|
||||
Volume = 11301.5139
|
||||
SHAKE stats (type/ave/delta) on step 35000
|
||||
2 1.08998 1.28162e-06
|
||||
4 0.944981 0
|
||||
5 0.999982 8.25561e-06
|
||||
6 109.47 0.000790911
|
||||
---------------- Step 35000 ----- CPU = 86.8870 (sec) ----------------
|
||||
TotEng = -3370.6689 KinEng = 637.0075 Temp = 294.0864
|
||||
PotEng = -4007.6763 E_bond = 0.2585 E_angle = 2.7426
|
||||
E_dihed = 0.2288 E_impro = 0.0000 E_vdwl = 766.3429
|
||||
E_coul = 14871.1344 E_long = -19648.3835 Press = -434.1739
|
||||
Volume = 11077.2342
|
||||
SHAKE stats (type/ave/delta) on step 40000
|
||||
2 1.09005 3.30799e-07
|
||||
4 0.945044 0
|
||||
5 1.00005 4.39187e-06
|
||||
6 109.47 0.000367325
|
||||
---------------- Step 40000 ----- CPU = 102.1257 (sec) ----------------
|
||||
TotEng = -3318.0442 KinEng = 694.3948 Temp = 320.5803
|
||||
PotEng = -4012.4390 E_bond = 0.3986 E_angle = 4.3594
|
||||
E_dihed = 1.0551 E_impro = 0.0000 E_vdwl = 716.6662
|
||||
E_coul = 14914.0530 E_long = -19648.9712 Press = -1177.4188
|
||||
Volume = 11087.6184
|
||||
SHAKE stats (type/ave/delta) on step 45000
|
||||
2 1.08997 7.63663e-06
|
||||
4 0.944973 0
|
||||
5 0.999973 2.30441e-05
|
||||
6 109.47 0.00155851
|
||||
---------------- Step 45000 ----- CPU = 119.3648 (sec) ----------------
|
||||
TotEng = -3371.5332 KinEng = 660.1645 Temp = 304.7773
|
||||
PotEng = -4031.6977 E_bond = 1.3352 E_angle = 2.6760
|
||||
E_dihed = 1.0255 E_impro = 0.0000 E_vdwl = 734.4320
|
||||
E_coul = 14878.0777 E_long = -19649.2440 Press = -978.3955
|
||||
Volume = 11108.5059
|
||||
SHAKE stats (type/ave/delta) on step 50000
|
||||
2 1.09015 1.28872e-06
|
||||
4 0.945128 0
|
||||
5 1.00014 5.27234e-06
|
||||
6 109.47 0.000408939
|
||||
---------------- Step 50000 ----- CPU = 132.4029 (sec) ----------------
|
||||
TotEng = -3345.1117 KinEng = 660.2366 Temp = 304.8106
|
||||
PotEng = -4005.3482 E_bond = 0.9878 E_angle = 3.3427
|
||||
E_dihed = 0.4740 E_impro = 0.0000 E_vdwl = 763.3350
|
||||
E_coul = 14874.5886 E_long = -19648.0763 Press = 257.8221
|
||||
Volume = 10750.8743
|
||||
SHAKE stats (type/ave/delta) on step 55000
|
||||
2 1.09006 1.79853e-06
|
||||
4 0.945055 0
|
||||
5 1.00006 8.96473e-06
|
||||
6 109.47 0.000604022
|
||||
---------------- Step 55000 ----- CPU = 144.3965 (sec) ----------------
|
||||
TotEng = -3329.0112 KinEng = 639.1918 Temp = 295.0949
|
||||
PotEng = -3968.2030 E_bond = 0.3779 E_angle = 4.2627
|
||||
E_dihed = 0.1647 E_impro = 0.0000 E_vdwl = 775.0143
|
||||
E_coul = 14900.7482 E_long = -19648.7708 Press = 384.3466
|
||||
Volume = 10943.9465
|
||||
SHAKE stats (type/ave/delta) on step 60000
|
||||
2 1.09006 5.76725e-07
|
||||
4 0.94505 0
|
||||
5 1.00005 4.15938e-06
|
||||
6 109.47 0.000456895
|
||||
---------------- Step 60000 ----- CPU = 158.9285 (sec) ----------------
|
||||
TotEng = -3337.6373 KinEng = 686.3391 Temp = 316.8613
|
||||
PotEng = -4023.9764 E_bond = 0.1951 E_angle = 3.2295
|
||||
E_dihed = 0.2227 E_impro = 0.0000 E_vdwl = 803.8460
|
||||
E_coul = 14822.5916 E_long = -19654.0613 Press = 343.2839
|
||||
Volume = 11053.5476
|
||||
SHAKE stats (type/ave/delta) on step 65000
|
||||
2 1.08992 1.92627e-06
|
||||
4 0.944928 0
|
||||
5 0.999925 9.65284e-06
|
||||
6 109.47 0.000982037
|
||||
---------------- Step 65000 ----- CPU = 171.6679 (sec) ----------------
|
||||
TotEng = -3286.1431 KinEng = 655.6296 Temp = 302.6837
|
||||
PotEng = -3941.7726 E_bond = 0.8912 E_angle = 5.2439
|
||||
E_dihed = 1.0392 E_impro = 0.0000 E_vdwl = 723.8338
|
||||
E_coul = 14977.3056 E_long = -19650.0863 Press = -610.8426
|
||||
Volume = 11125.9793
|
||||
SHAKE stats (type/ave/delta) on step 70000
|
||||
2 1.08995 3.49023e-07
|
||||
4 0.944954 0
|
||||
5 0.999952 3.62092e-06
|
||||
6 109.47 0.000402967
|
||||
---------------- Step 70000 ----- CPU
|
||||
|
|
@ -0,0 +1,22 @@
|
|||
# Time-averaged data for fix fFEP
|
||||
# TimeStep c_cFEP[1] c_cFEP[2]
|
||||
125000 1.6302 0.0823708
|
||||
250000 1.42237 0.11283
|
||||
375000 1.1798 0.168088
|
||||
500000 0.869449 0.279336
|
||||
625000 0.610803 0.412455
|
||||
750000 0.489597 0.486584
|
||||
875000 0.34439 0.601048
|
||||
1000000 0.303411 0.640696
|
||||
1125000 0.244627 0.70206
|
||||
1250000 0.204737 0.746389
|
||||
1375000 0.144716 0.816302
|
||||
1500000 0.0941156 0.880968
|
||||
1625000 0.0575351 0.933564
|
||||
1750000 0.0171831 0.992497
|
||||
1875000 -0.018964 1.05078
|
||||
2000000 -0.0457397 1.09726
|
||||
2125000 -0.0904898 1.17888
|
||||
2250000 -0.128205 1.25226
|
||||
2375000 -0.155891 1.31122
|
||||
2500000 -0.194237 1.3965
|
||||
|
|
@ -0,0 +1,142 @@
|
|||
# created by fftool
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
read_data data.1.lmp
|
||||
# read_restart restart.*.lmp
|
||||
# reset_timestep 0
|
||||
|
||||
pair_style hybrid lj/cut/coul/long 10.0 10.0 &
|
||||
lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
|
||||
pair_modify tail no
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
pair_coeff 1 1 none # CO-C CO-C
|
||||
pair_coeff 1 2 none # CO-C CD-
|
||||
pair_coeff 1 3 none # CO-C HD-
|
||||
pair_coeff 1 4 none # CO-C H1-H
|
||||
pair_coeff 1 5 none # CO-C OH-D
|
||||
pair_coeff 1 6 none # CO-C HO-D
|
||||
pair_coeff 1 7 lj/cut/coul/long 0.0000 1.0000 # CO-C Hw
|
||||
pair_coeff 1 8 lj/cut/coul/long 0.1013 3.3286 # CO-C Ow
|
||||
pair_coeff 2 2 none # CD- CD-
|
||||
pair_coeff 2 3 none # CD- HD-
|
||||
pair_coeff 2 4 none # CD- H1-H
|
||||
pair_coeff 2 5 none # CD- OH-D
|
||||
pair_coeff 2 6 none # CD- HO-D
|
||||
pair_coeff 2 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # CD- Hw
|
||||
pair_coeff 2 8 lj/cut/coul/long/soft 0.1013 3.3286 0.0 # CD- Ow
|
||||
pair_coeff 3 3 none # HD- HD-
|
||||
pair_coeff 3 4 lj/cut/coul/long/soft 0.0300 2.5000 0.0 # HD- H1-H
|
||||
pair_coeff 3 5 none # HD- OH-D
|
||||
pair_coeff 3 6 none # HD- HO-D
|
||||
pair_coeff 3 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # HD- Hw
|
||||
pair_coeff 3 8 lj/cut/coul/long/soft 0.0683 2.8131 0.0 # HD- Ow
|
||||
pair_coeff 4 4 none # H1-H H1-H
|
||||
pair_coeff 4 5 none # H1-H OH-D
|
||||
pair_coeff 4 6 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # H1-H HO-D
|
||||
pair_coeff 4 7 lj/cut/coul/long 0.0000 1.0000 # H1-H Hw
|
||||
pair_coeff 4 8 lj/cut/coul/long 0.0683 2.8131 # H1-H Ow
|
||||
pair_coeff 5 5 none # OH-D OH-D
|
||||
pair_coeff 5 6 none # OH-D HO-D
|
||||
pair_coeff 5 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # OH-D Hw
|
||||
pair_coeff 5 8 lj/cut/coul/long/soft 0.1625 3.1427 1.0 # OH-D Ow
|
||||
pair_coeff 6 6 none # HO-D HO-D
|
||||
pair_coeff 6 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # HO-D Hw
|
||||
pair_coeff 6 8 lj/cut/coul/long/soft 0.0000 1.7792 1.0 # HO-D Ow
|
||||
pair_coeff 7 7 lj/cut/coul/long 0.0000 1.0000 # Hw Hw
|
||||
pair_coeff 7 8 lj/cut/coul/long 0.0000 1.0000 # Hw Ow
|
||||
pair_coeff 8 8 lj/cut/coul/long 0.1554 3.1655 # Ow Ow
|
||||
|
||||
variable nsteps equal 2500000
|
||||
variable nprint equal ${nsteps}/500
|
||||
variable ndump equal ${nsteps}/100
|
||||
# variable nrestart equal ${nsteps}/10
|
||||
|
||||
variable temp equal 300.0
|
||||
variable press equal 1.0
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
timestep 2.0
|
||||
|
||||
velocity all create ${temp} 12345
|
||||
|
||||
thermo_style multi
|
||||
thermo ${nprint}
|
||||
|
||||
fix fSHAKE all shake 0.0001 20 ${nprint} b 2 4 5 a 6
|
||||
|
||||
fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 500
|
||||
|
||||
run 250000
|
||||
reset_timestep 0
|
||||
|
||||
|
||||
variable lambda equal ramp(1.0,0.0)
|
||||
variable minusl equal 1.0-v_lambda
|
||||
variable q1 equal 0.145*v_lambda-0.180*(1.0-v_lambda)
|
||||
variable q2 equal -0.180*(1.0-v_lambda)
|
||||
variable q3 equal 0.060*(1.0-v_lambda)
|
||||
variable q4 equal 0.040*v_lambda+0.060*(1.0-v_lambda)
|
||||
variable q5 equal -0.683*v_lambda
|
||||
variable q6 equal 0.418*v_lambda
|
||||
|
||||
fix fADAPT all adapt/fep 125000 &
|
||||
pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusl &
|
||||
pair lj/cut/coul/long/soft lambda 3 4 v_minusl &
|
||||
pair lj/cut/coul/long/soft lambda 4 6 v_lambda &
|
||||
pair lj/cut/coul/long/soft lambda 5*6 7*8 v_lambda &
|
||||
atom charge 1 v_q1 &
|
||||
atom charge 2 v_q2 &
|
||||
atom charge 3 v_q3 &
|
||||
atom charge 4 v_q4 &
|
||||
atom charge 5 v_q5 &
|
||||
atom charge 6 v_q6 &
|
||||
after yes
|
||||
|
||||
variable dlambda equal -0.05
|
||||
variable minusdl equal 0.05
|
||||
variable dq1 equal 0.145*v_dlambda+0.180*v_dlambda
|
||||
variable dq2 equal 0.180*v_dlambda
|
||||
variable dq3 equal -0.060*v_dlambda
|
||||
variable dq4 equal 0.040*v_dlambda-0.060*v_dlambda
|
||||
variable dq5 equal -0.683*v_dlambda
|
||||
variable dq6 equal 0.418*v_dlambda
|
||||
|
||||
compute cFEP all fep ${temp} &
|
||||
pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusdl &
|
||||
pair lj/cut/coul/long/soft lambda 3 4 v_minusdl &
|
||||
pair lj/cut/coul/long/soft lambda 4 6 v_dlambda &
|
||||
pair lj/cut/coul/long/soft lambda 5*6 7*8 v_dlambda &
|
||||
atom charge 1 v_dq1 &
|
||||
atom charge 2 v_dq2 &
|
||||
atom charge 3 v_dq3 &
|
||||
atom charge 4 v_dq4 &
|
||||
atom charge 5 v_dq5 &
|
||||
atom charge 6 v_dq6
|
||||
|
||||
fix fFEP all ave/time 25 4000 125000 c_cFEP[1] c_cFEP[2] file fep10.lmp
|
||||
|
||||
# compute cRDF all rdf 100 1 1
|
||||
# fix fRDF all ave/time 20 100 ${nsteps} c_cRDF file rdf.lammps mode vector
|
||||
|
||||
compute cMSD all msd
|
||||
fix fMSD all ave/time 1 1 ${ndump} c_cMSD[1] c_cMSD[2] c_cMSD[3] c_cMSD[4] file msd.lammps
|
||||
|
||||
dump dCONF all custom ${ndump} dump.lammpstrj id mol type element x y z ix iy iz
|
||||
dump_modify dCONF element C C H H O H H O
|
||||
|
||||
# restart ${nrestart} restart.*.lmp
|
||||
|
||||
run ${nsteps}
|
||||
|
||||
write_restart restart.*.lmp
|
||||
write_data data.*.lmp
|
||||
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,49 @@
|
|||
# CC-CO.ff (kJ/mol, A, deg)
|
||||
|
||||
ATOMS
|
||||
# type m/uma q/e pot pars
|
||||
# ethane OPLS-AA
|
||||
C-CO CT 12.011 -0.180 lj 3.50 0.27614
|
||||
C-D CT 12.011 -0.180 lj 3.50 0.27614
|
||||
CD- CT 12.011 0.000 lj 3.50 0.27614
|
||||
H-D HC 1.008 0.060 lj 2.50 0.12552
|
||||
HD- HC 1.008 0.000 lj 2.50 0.12552
|
||||
H-H1 HC 1.008 0.060 lj 2.50 0.12552
|
||||
# methanol OPLS-AA
|
||||
CO-C CT 12.011 0.145 lj 3.50 0.27614
|
||||
H1-H HC 1.008 0.040 lj 2.50 0.12552
|
||||
OH-D OH 15.999 -0.683 lj 3.12 0.71128
|
||||
OHD- OH 15.999 0.000 lj 3.12 0.71128
|
||||
HO-D HO 1.008 0.418 lj 1.00 0.00000
|
||||
HOD- HO 1.008 0.000 lj 1.00 0.00000
|
||||
|
||||
BONDS
|
||||
# i j pot re/A ka/kJmol-1
|
||||
# alkanes OPLS-AA JACS 118(1996)11225, JPC 100(1996)18010
|
||||
HC CT cons 1.090 2845.12
|
||||
CT CT harm 1.529 2242.62
|
||||
# alcohols OPLS-AA JACS 118(1996)11225, JPC 100(1996)18010
|
||||
CT OH harm 1.410 2677.76
|
||||
HO OH cons 0.945 4627.50
|
||||
|
||||
ANGLES
|
||||
# i j k pot th/deg ka/kjmol-1
|
||||
# alkanes OPLS-AA JACS 118(1996)11225, JPC 100(1996)18010
|
||||
HC CT HC harm 107.80 276.14
|
||||
HC CT CT harm 110.70 313.80
|
||||
CT CT CT harm 112.70 488.27
|
||||
# alcohols OPLS-AA JACS 118(1996)11225, JPC 100(1996)18010
|
||||
CT CT OH harm 0.0 418.40
|
||||
HC CT OH harm 109.50 292.88
|
||||
CT OH HO harm 108.50 460.24
|
||||
|
||||
DIHEDRALS
|
||||
# i j k l pot v1 v2 v3 v4
|
||||
# alkanes OPLS-AA JACS 118: 11225 (1996); J Phys Chem 100: 18010 (1996)
|
||||
HC CT CT HC opls 0.0000 0.0000 1.3305 0.0000
|
||||
HC CT CT CT opls 0.0000 0.0000 1.5313 0.0000
|
||||
CT CT CT CT opls 7.2800 -0.6569 1.1673 0.0000
|
||||
# alcohols OPLS-AA JACS 118(1996)11225, AMBER98 (OCCO) 117(1995)5179
|
||||
HC CT OH HO opls 0.0000 0.0000 1.8828 0.0000
|
||||
CT CT OH HO opls 0.0000 0.0000 0.0000 0.0000
|
||||
HC CT CT OH opls 0.0000 0.0000 0.0000 0.0000
|
||||
|
|
@ -0,0 +1,14 @@
|
|||
CC->CO
|
||||
|
||||
1 C-CO
|
||||
2 C-D 1 1.529
|
||||
3 H-D 2 1.090 1 109.5
|
||||
4 H-D 2 1.090 1 109.5 3 120.0
|
||||
5 H-D 2 1.090 1 109.5 3 240.0
|
||||
6 H-H1 1 1.090 2 109.5 3 180.0
|
||||
7 H-H1 1 1.090 2 109.5 4 180.0
|
||||
8 H-H1 1 1.090 2 109.5 5 180.0
|
||||
9 OHD- 1 1.410 2 1.0 3 0.0
|
||||
10 HOD- 9 0.945 1 109.5 2 180.0
|
||||
|
||||
CC-CO.ff
|
||||
|
|
@ -0,0 +1,14 @@
|
|||
CO->CC
|
||||
|
||||
1 CO-C
|
||||
2 CD- 1 1.529
|
||||
3 HD- 2 1.090 1 109.5
|
||||
4 HD- 2 1.090 1 109.5 3 120.0
|
||||
5 HD- 2 1.090 1 109.5 3 240.0
|
||||
6 H1-H 1 1.090 2 109.5 3 180.0
|
||||
7 H1-H 1 1.090 2 109.5 4 180.0
|
||||
8 H1-H 1 1.090 2 109.5 5 180.0
|
||||
9 OH-D 1 1.410 2 1.0 3 0.0
|
||||
10 HO-D 9 0.945 1 109.5 2 180.0
|
||||
|
||||
CC-CO.ff
|
||||
|
|
@ -0,0 +1,15 @@
|
|||
Ethane to Methanol Molecule Files
|
||||
=================================
|
||||
|
||||
Files necessary to build starting configurations using the
|
||||
[fftool.py](http://www.github.com/agiliopadua/fftool) utility and
|
||||
[Packmol](http://www.ime.unicamp.br/~martinez/packmol/), for example:
|
||||
|
||||
fftool.py 1 CC-CO.zmat 360 spce.zmat -r 50
|
||||
|
||||
packmol < pack.in
|
||||
|
||||
fftool.py 1 CC-CO.zmat 360 spce.zmat -r 50 -l -a
|
||||
|
||||
The resulting `in.lmp` files have to be modified to introduce the free
|
||||
energy route.
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,14 @@
|
|||
# SPC/E water (kJ/mol, A, deg)
|
||||
|
||||
ATOMS
|
||||
# type m/uma q/e pot pars
|
||||
Ow Ow 15.999 -0.8476 lj 3.1655 0.6503
|
||||
Hw Hw 1.008 0.4238 lj 1.0000 0.0000
|
||||
|
||||
BONDS
|
||||
# i j pot re/A ka/kJmol-1
|
||||
Ow Hw cons 1.000 4331.53
|
||||
|
||||
ANGLES
|
||||
# i j k pot th/deg ka/kjmol-1
|
||||
Hw Ow Hw cons 109.47 317.57
|
||||
|
|
@ -0,0 +1,7 @@
|
|||
SPCE
|
||||
|
||||
Hw
|
||||
Ow 1 1.000
|
||||
Hw 2 1.000 1 109.47
|
||||
|
||||
spce.ff
|
||||
|
|
@ -0,0 +1,57 @@
|
|||
Methane to Tetrafluoromethane in Water
|
||||
======================================
|
||||
|
||||
Example calculation of the difference in free energy of hydration upon
|
||||
transforming methane into tetrafluoromethane with LAMMPS using
|
||||
*compute fep* and *fix adapt*.
|
||||
|
||||
Methane and tetrafluoromethane are represented by the OPLS-AA force
|
||||
field (1 molecule). Water is represented by the 3-site SPC/E model
|
||||
(360 molecules).
|
||||
|
||||
The strategy used to perform the alchemical transformation is the
|
||||
following:
|
||||
|
||||
* The dual topology approach is used, therefore all the atoms of
|
||||
methane and perfluorommethane are present throughout the simulation,
|
||||
only some of them are dummy sites at the endpoints of the
|
||||
transformation. Masses and intramolecular terms (bond lengths,
|
||||
angles, dihedrals) are not changed.
|
||||
|
||||
* Interactions of sites that are being created (from dummy sites) or
|
||||
deleted (to become dummy sites) are treated using soft-core verions
|
||||
of the Lennard-Jones and Coulomb potentials (*pair
|
||||
lj/cut/coul/long/soft*) in order to avoid singularities. The
|
||||
exponent of the coupling parameter lambda in the soft-core pair
|
||||
potentials was in this example n = 1.
|
||||
|
||||
* Eletrostatic charges that are modified are varied linearly from the
|
||||
initial to the final values. This keeps the overall charge of the
|
||||
molecule constant, which is good for the long range electrostatics
|
||||
(the coupling parameter lambda has no effect on the kspace terms).
|
||||
|
||||
The following directories contain input files and results for
|
||||
calculations using Bennet's acceptance ratio (BAR) method:
|
||||
|
||||
* `bar01` -- Calculation using BAR, 1-step transformation of a CH4
|
||||
molecule into CF4. Results in `bar01.lmp`
|
||||
|
||||
* `bar10` -- Calculation using BAR, 1-step transformation of a
|
||||
CF4 molecule into CH4. Results in `bar10.lmp`
|
||||
|
||||
The Python script `bar.py` found in the `tools` directory can
|
||||
be used to calculate the free-energy difference corresponding to the
|
||||
transformation:
|
||||
|
||||
bar.py 300 bar01.lmp bar10.lmp
|
||||
|
||||
The outputs are in kcal/mol and can be compared with the experimental
|
||||
value of 1.2 kcal/mol and with a simulation value from the literature
|
||||
(using a different force field): 0.8 kcal/mol
|
||||
[Gough, Pearlman, Kolmann, J Chem Phys 99 (1993) 9103]. This small
|
||||
free energy difference is difficult to predict.
|
||||
|
||||
These example calculations are for tutorial purposes only. The results
|
||||
may not be of research quality (not enough sampling, size of the step
|
||||
in lambda or of the delta for numerical derivative not optimized, no
|
||||
evaluation of ideal-gas contributions, etc.)
|
||||
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,89 @@
|
|||
# created by fftool
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
read_data data.0.lmp
|
||||
# read_restart restart.*.lmp
|
||||
# reset_timestep 0
|
||||
|
||||
pair_style hybrid lj/cut/coul/long 10.0 10.0 lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
|
||||
pair_modify tail yes
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
pair_coeff 1 1 none # C-CF C-CF
|
||||
pair_coeff 1 2 none # C-CF H-D
|
||||
pair_coeff 1 3 none # C-CF FD-
|
||||
pair_coeff 1 4 lj/cut/coul/long 0.0000 1.8708 # C-CF Hw
|
||||
pair_coeff 1 5 lj/cut/coul/long 0.1013 3.3286 # C-CF Ow
|
||||
pair_coeff 2 2 none # H-D H-D
|
||||
pair_coeff 2 3 none # H-D FD-
|
||||
pair_coeff 2 4 lj/cut/coul/long/soft 0.0000 1.5811 1.0 # H-D Hw
|
||||
pair_coeff 2 5 lj/cut/coul/long/soft 0.0683 2.8131 1.0 # H-D Ow
|
||||
pair_coeff 3 3 none # FD- FD-
|
||||
pair_coeff 3 4 lj/cut/coul/long/soft 0.0000 1.7176 0.0 # FD- Hw
|
||||
pair_coeff 3 5 lj/cut/coul/long/soft 0.0908 3.0559 0.0 # FD- Ow
|
||||
pair_coeff 4 4 lj/cut/coul/long 0.0000 1.0000 # Hw Hw
|
||||
pair_coeff 4 5 lj/cut/coul/long 0.0000 1.7792 # Hw Ow
|
||||
pair_coeff 5 5 lj/cut/coul/long 0.1554 3.1655 # Ow Ow
|
||||
|
||||
variable nsteps equal 500000
|
||||
variable nprint equal ${nsteps}/500
|
||||
variable ndump equal ${nsteps}/100
|
||||
# variable nrestart equal ${nsteps}/10
|
||||
|
||||
variable temp equal 300.0
|
||||
variable press equal 1.0
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
timestep 2.0
|
||||
|
||||
velocity all create ${temp} 12345
|
||||
|
||||
thermo_style multi
|
||||
thermo ${nprint}
|
||||
|
||||
fix fSHAKE all shake 0.0001 20 ${nprint} b 3 a 4
|
||||
|
||||
fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 500
|
||||
|
||||
run 200000
|
||||
reset_timestep 0
|
||||
|
||||
variable dlambda equal 1.0
|
||||
variable minusdl equal -1.0
|
||||
variable dqC equal 0.48*v_dlambda-0.24*(1.0-v_dlambda)
|
||||
variable dqH equal 0.06*(1.0-v_dlambda)
|
||||
variable dqF equal -0.12*v_dlambda
|
||||
|
||||
compute cFEP all fep ${temp} &
|
||||
pair lj/cut/coul/long/soft lambda 2 4*5 v_minusdl &
|
||||
pair lj/cut/coul/long/soft lambda 3 4*5 v_dlambda &
|
||||
atom charge 1 v_dqC &
|
||||
atom charge 2 v_dqH &
|
||||
atom charge 3 v_dqF
|
||||
|
||||
fix fFEP all ave/time 1 1 100 c_cFEP[1] c_cFEP[2] file bar01.lmp
|
||||
|
||||
|
||||
# compute cRDF all rdf 100 1 1
|
||||
# fix fRDF all ave/time 20 100 ${nsteps} c_cRDF file rdf.lammps mode vector
|
||||
|
||||
# compute cMSD all msd
|
||||
# fix fMSD all ave/time 1 1 ${ndump} c_cMSD[1] c_cMSD[2] c_cMSD[3] c_cMSD[4] file msd.lammps
|
||||
|
||||
dump dCONF all custom ${ndump} dump.lammpstrj id mol type element x y z ix iy iz
|
||||
dump_modify dCONF element C H F H O
|
||||
|
||||
# restart ${nrestart} restart.*.lmp
|
||||
|
||||
run ${nsteps}
|
||||
|
||||
# write_restart restart.*.lmp
|
||||
write_data data.*.lmp
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,89 @@
|
|||
# created by fftool
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
read_data data.1.lmp
|
||||
# read_restart restart.*.lmp
|
||||
# reset_timestep 0
|
||||
|
||||
pair_style hybrid lj/cut/coul/long 10.0 10.0 lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
|
||||
pair_modify tail yes
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
pair_coeff 1 1 none # CF-C CF-C
|
||||
pair_coeff 1 2 none # CF-C HD-
|
||||
pair_coeff 1 3 none # CF-C F-D
|
||||
pair_coeff 1 4 lj/cut/coul/long 0.0000 1.8708 # CF-C Hw
|
||||
pair_coeff 1 5 lj/cut/coul/long 0.1013 3.3286 # CF-C Ow
|
||||
pair_coeff 2 2 none # HD- HD-
|
||||
pair_coeff 2 3 none # HD- F-D
|
||||
pair_coeff 2 4 lj/cut/coul/long/soft 0.0000 1.5811 0.0 # HD- Hw
|
||||
pair_coeff 2 5 lj/cut/coul/long/soft 0.0683 2.8131 0.0 # HD- Ow
|
||||
pair_coeff 3 3 none # F-D F-D
|
||||
pair_coeff 3 4 lj/cut/coul/long/soft 0.0000 1.7176 1.0 # F-D Hw
|
||||
pair_coeff 3 5 lj/cut/coul/long/soft 0.0908 3.0559 1.0 # F-D Ow
|
||||
pair_coeff 4 4 lj/cut/coul/long 0.0000 1.0000 # Hw Hw
|
||||
pair_coeff 4 5 lj/cut/coul/long 0.0000 1.7792 # Hw Ow
|
||||
pair_coeff 5 5 lj/cut/coul/long 0.1554 3.1655 # Ow Ow
|
||||
|
||||
variable nsteps equal 500000
|
||||
variable nprint equal ${nsteps}/500
|
||||
variable ndump equal ${nsteps}/100
|
||||
# variable nrestart equal ${nsteps}/10
|
||||
|
||||
variable temp equal 300.0
|
||||
variable press equal 1.0
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
timestep 2.0
|
||||
|
||||
velocity all create ${temp} 12345
|
||||
|
||||
thermo_style multi
|
||||
thermo ${nprint}
|
||||
|
||||
fix fSHAKE all shake 0.0001 20 ${nprint} b 3 a 4
|
||||
|
||||
fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 500
|
||||
|
||||
run 200000
|
||||
reset_timestep 0
|
||||
|
||||
variable dlambda equal 1.0
|
||||
variable minusdl equal -1.0
|
||||
variable dqC equal -0.24*v_dlambda+0.48*(1.0-v_dlambda)
|
||||
variable dqH equal 0.06*v_dlambda
|
||||
variable dqF equal -0.12*(1.0-v_dlambda)
|
||||
|
||||
compute cFEP all fep ${temp} &
|
||||
pair lj/cut/coul/long/soft lambda 2 4*5 v_dlambda &
|
||||
pair lj/cut/coul/long/soft lambda 3 4*5 v_minusdl &
|
||||
atom charge 1 v_dqC &
|
||||
atom charge 2 v_dqH &
|
||||
atom charge 3 v_dqF
|
||||
|
||||
fix fFEP all ave/time 1 1 100 c_cFEP[1] c_cFEP[2] file bar10.lmp
|
||||
|
||||
|
||||
# compute cRDF all rdf 100 1 1
|
||||
# fix fRDF all ave/time 20 100 ${nsteps} c_cRDF file rdf.lammps mode vector
|
||||
|
||||
# compute cMSD all msd
|
||||
# fix fMSD all ave/time 1 1 ${ndump} c_cMSD[1] c_cMSD[2] c_cMSD[3] c_cMSD[4] file msd.lammps
|
||||
|
||||
dump dCONF all custom ${ndump} dump.lammpstrj id mol type element x y z ix iy iz
|
||||
dump_modify dCONF element C H F H O
|
||||
|
||||
# restart ${nrestart} restart.*.lmp
|
||||
|
||||
run ${nsteps}
|
||||
|
||||
# write_restart restart.*.lmp
|
||||
write_data data.*.lmp
|
||||
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,16 @@
|
|||
CF4->CH4
|
||||
|
||||
1 CF-C
|
||||
2 HD- 1 rCH
|
||||
3 HD- 1 rCH 2 109.5
|
||||
4 HD- 1 rCH 2 109.5 3 120.0
|
||||
5 HD- 1 rCH 2 109.5 3 -120.0
|
||||
6 F-D 1 rCF 2 109.5 3 -120.0
|
||||
7 F-D 1 rCF 2 109.5 3 120.0
|
||||
8 F-D 1 rCF 7 109.5 5 120.0
|
||||
9 F-D 1 rCF 7 109.5 5 -120.0
|
||||
|
||||
rCH = 1.090
|
||||
rCF = 1.332
|
||||
|
||||
CH4-CF4.ff
|
||||
|
|
@ -0,0 +1,28 @@
|
|||
# oplsaa.ff (kJ/mol, A, deg) version 2013/12/07
|
||||
|
||||
ATOMS
|
||||
# type m/uma q/e pot pars
|
||||
# alkanes JACS 118(1996)11225, JPC 100(1996)18010
|
||||
C-CF CT 12.011 -0.24 lj 3.50 0.27614
|
||||
H-D HC 6.008 0.06 lj 2.50 0.12552
|
||||
HD- HC 6.008 0.00 lj 2.50 0.12552
|
||||
# perfluoroalkanes JPCA105:4118(2001)
|
||||
CF-C CT 12.011 0.48 lj 3.50 0.27614
|
||||
FD- F 18.998 0.00 lj 2.95 0.22175
|
||||
F-D F 18.998 -0.12 lj 2.95 0.22175
|
||||
|
||||
BONDS
|
||||
# i j pot re/A ka/kJmol-1
|
||||
# alkanes OPLS-AA JACS 118(1996)11225, JPC 100(1996)18010
|
||||
HC CT harm 1.090 2845.12
|
||||
# perfluoroalkanes JPCA105(2001)4118
|
||||
F CT harm 1.332 3071.1
|
||||
|
||||
ANGLES
|
||||
# i j k pot th/deg ka/kjmol-1
|
||||
# alkanes JACS 118(1996)11225, JPC 100(1996)18010
|
||||
HC CT HC harm 107.80 276.14
|
||||
# perfluorocarbons JPCA105(2001)4118
|
||||
F CT F harm 109.1 644.3
|
||||
# special
|
||||
HC CT F harm 0.0 0.0
|
||||
|
|
@ -0,0 +1,16 @@
|
|||
CH4->CF4
|
||||
|
||||
1 C-CF
|
||||
2 H-D 1 rCH
|
||||
3 H-D 1 rCH 2 109.5
|
||||
4 H-D 1 rCH 2 109.5 3 120.0
|
||||
5 H-D 1 rCH 2 109.5 3 -120.0
|
||||
6 FD- 1 rCF 2 109.5 3 -120.0
|
||||
7 FD- 1 rCF 2 109.5 3 120.0
|
||||
8 FD- 1 rCF 7 109.5 5 120.0
|
||||
9 FD- 1 rCF 7 109.5 5 -120.0
|
||||
|
||||
rCH = 1.090
|
||||
rCF = 1.332
|
||||
|
||||
CH4-CF4.ff
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,14 @@
|
|||
# SPC/E water (kJ/mol, A, deg)
|
||||
|
||||
ATOMS
|
||||
# type m/uma q/e pot pars
|
||||
Ow Ow 15.999 -0.8476 lj 3.1655 0.6503
|
||||
Hw Hw 1.008 0.4238 lj 1.0000 0.0000
|
||||
|
||||
BONDS
|
||||
# i j pot re/A ka/kJmol-1
|
||||
Ow Hw cons 1.000 4331.53
|
||||
|
||||
ANGLES
|
||||
# i j k pot th/deg ka/kjmol-1
|
||||
Hw Ow Hw cons 109.47 317.57
|
||||
|
|
@ -0,0 +1,7 @@
|
|||
SPCE
|
||||
|
||||
Hw
|
||||
Ow 1 1.000
|
||||
Hw 2 1.000 1 109.47
|
||||
|
||||
spce.ff
|
||||
|
|
@ -0,0 +1,59 @@
|
|||
Free Energy of Hydration of Methane
|
||||
===================================
|
||||
|
||||
Example calculation of the free energy of hydration of methane with
|
||||
LAMMPS using *compute fep* and *fix adapt/fep*.
|
||||
|
||||
Methane is represented by the 5-site OPLS-AA model (1 molecule). Water
|
||||
is represented by the 4-site TIP4P-Ew model (360 molecules). Interactions
|
||||
of sites that are being created or deleted are treated using soft-core
|
||||
verions of the Lennard-Jones and Coulomb potentials (*pair
|
||||
lj/cut/coul/long/soft*) in order to avoid singularities.
|
||||
|
||||
The following directories contain input files and results for
|
||||
calculations using free-energy perturbation (FEP) and
|
||||
finite-difference thermodynamic integration (FDTI):
|
||||
|
||||
* `mols` -- molecule description files and force field database used
|
||||
to create the initial configuration used for the simulations
|
||||
`data.lmp`
|
||||
|
||||
* `fep01` -- Calculation using FEP, multi-stage creation of a methane
|
||||
molecule. Results in `fep01.lmp`
|
||||
|
||||
* `fep10` -- Calculation using FEP, multi-stage deletion of a methane
|
||||
molecule. Results in `fep10.lmp`
|
||||
|
||||
* `fdti01` -- Calculation using TI/FDTI, creation of a methane
|
||||
molecule. Results in `fdti01.lmp`
|
||||
|
||||
* `fdti10` -- Calculation using TI/FDTI, deletion a methane
|
||||
molecule. Results in `fdti10.lmp`
|
||||
|
||||
The free-energy profiles can be observed by plotting the values in the
|
||||
third column of the results files. The Python scripts `fep.py`,
|
||||
`nti.py` and `fdti.py` found in the `tools` directory can be used to
|
||||
calculate the free-energy differences corresponding to the above
|
||||
transformations:
|
||||
|
||||
fep.py 300 < fep01.lmp
|
||||
|
||||
fep.py 300 < fep10.lmp
|
||||
|
||||
nti.py 300 0.002 < fdti01.lmp
|
||||
|
||||
nti.py 300 0.002 < fdti10.lmp
|
||||
|
||||
fdti.py 300 0.002 < fdti01.lmp
|
||||
|
||||
fdti.py 300 0.002 < fdti10.lmp
|
||||
|
||||
The outputs are in kcal/mol and can be compared with the experimental
|
||||
value of 2.0 kcal/mol, or with a simulation value from the literature
|
||||
obtained with the same force field models used here: 2.27 kcal/mol
|
||||
[MR Shirts, VS Pande, J Chem Phys 122 (2005) 134508].
|
||||
|
||||
These example calculations are for tutorial purposes only. The results
|
||||
may not be of research quality (not enough sampling, size of the step
|
||||
in lambda or of the delta for numerical derivative not optimized, no
|
||||
evaluation of ideal-gas contributions, etc.)
|
||||
|
|
@ -0,0 +1,22 @@
|
|||
# Time-averaged data for fix fFEP
|
||||
# TimeStep c_cFEP[1] c_cFEP[2]
|
||||
125000 0.000490778 0.999186
|
||||
250000 0.00619786 0.989679
|
||||
375000 0.0128045 0.978813
|
||||
500000 0.0203102 0.96667
|
||||
625000 0.0272161 0.955808
|
||||
750000 0.0215735 0.965087
|
||||
875000 0.0148509 0.975821
|
||||
1000000 0.00936378 0.984752
|
||||
1125000 0.00490088 0.992007
|
||||
1250000 0.00388501 0.99366
|
||||
1375000 0.00122887 0.998043
|
||||
1500000 0.000498063 0.999247
|
||||
1625000 -0.000468616 1.00085
|
||||
1750000 -0.00131731 1.00226
|
||||
1875000 -0.00247035 1.00419
|
||||
2000000 -0.00306799 1.00519
|
||||
2125000 -0.00355565 1.006
|
||||
2250000 -0.00434289 1.00733
|
||||
2375000 -0.00497634 1.00839
|
||||
2500000 -0.00576373 1.00972
|
||||
|
|
@ -0,0 +1,80 @@
|
|||
# created by fftool
|
||||
|
||||
print "Methane in TIP4P water"
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
read_data data.lmp
|
||||
|
||||
pair_style hybrid &
|
||||
lj/cut/coul/long 10.0 10.0 &
|
||||
lj/cut/tip4p/long/soft 3 4 2 2 0.125 1 0.5 10.0 10.0 10.0
|
||||
pair_modify tail no
|
||||
kspace_style pppm/tip4p 1.0e-4
|
||||
|
||||
pair_coeff 1 1 lj/cut/coul/long 0.0660 3.5000 # C4H C4H
|
||||
pair_coeff 1 2 lj/cut/coul/long 0.0445 2.9580 # C4H H
|
||||
pair_coeff 2 2 lj/cut/coul/long 0.0300 2.5000 # H H
|
||||
pair_coeff 3 3 lj/cut/tip4p/long/soft 0.1628 3.1644 1.0 # Ow Ow
|
||||
pair_coeff 3 4 lj/cut/tip4p/long/soft 0.0000 1.0000 1.0 # Ow Hw
|
||||
pair_coeff 4 4 lj/cut/tip4p/long/soft 0.0000 1.0000 1.0 # Hw Hw
|
||||
|
||||
pair_coeff 1 3 lj/cut/tip4p/long/soft 0.1036 3.3279 0.0 # C4H Ow
|
||||
pair_coeff 1 4 lj/cut/tip4p/long/soft 0.0000 1.0000 0.0 # C4H Hw
|
||||
pair_coeff 2 3 lj/cut/tip4p/long/soft 0.0699 2.8126 0.0 # H Ow
|
||||
pair_coeff 2 4 lj/cut/tip4p/long/soft 0.0000 1.0000 0.0 # H Hw
|
||||
|
||||
variable nsteps equal 2500000
|
||||
variable nprint equal ${nsteps}/500
|
||||
variable ndump equal ${nsteps}/100
|
||||
|
||||
variable temp equal 300.0
|
||||
variable press equal 1.0
|
||||
|
||||
fix fSHAKE all shake 0.0001 20 ${nprint} b 2 a 2
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
timestep 2.0
|
||||
|
||||
velocity all create ${temp} 12345
|
||||
|
||||
thermo_style multi
|
||||
thermo ${nprint}
|
||||
|
||||
fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 1000
|
||||
|
||||
run 250000
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
variable lambda equal ramp(0.0,1.0)
|
||||
|
||||
fix fADAPT all adapt/fep 125000 pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_lambda after yes
|
||||
|
||||
variable dlambda equal 0.002
|
||||
|
||||
compute cFEP all fep ${temp} pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_dlambda
|
||||
|
||||
fix fFEP all ave/time 25 4000 125000 c_cFEP[1] c_cFEP[2] file fdti01.lmp
|
||||
|
||||
# compute cRDF all rdf 100 3 3 3 4 4 4
|
||||
# fix fRDF all ave/time 2000 500 ${nsteps} c_cRDF file rdf.lammps mode vector
|
||||
|
||||
group owater type 3
|
||||
compute cMSD owater msd
|
||||
fix fMSD owater ave/time 1 1 ${ndump} c_cMSD[1] c_cMSD[2] c_cMSD[3] c_cMSD[4] file msd.lammps
|
||||
|
||||
dump dCONF all custom ${ndump} dump.lammpstrj id mol type element x y z ix iy iz
|
||||
dump_modify dCONF element C H O H
|
||||
|
||||
run ${nsteps}
|
||||
|
||||
# write_restart restart.*.lmp
|
||||
write_data data.*.lmp
|
||||
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,22 @@
|
|||
# Time-averaged data for fix fFEP
|
||||
# TimeStep c_cFEP[1] c_cFEP[2]
|
||||
125000 0.00652155 0.989123
|
||||
250000 0.00572718 0.990445
|
||||
375000 0.00506788 0.991544
|
||||
500000 0.00448303 0.992522
|
||||
625000 0.00370796 0.993818
|
||||
750000 0.00277535 0.995385
|
||||
875000 0.00230833 0.996171
|
||||
1000000 0.000982551 0.998409
|
||||
1125000 0.000314678 0.99954
|
||||
1250000 -0.000839025 1.0015
|
||||
1375000 -0.00155615 1.00273
|
||||
1500000 -0.00320598 1.00553
|
||||
1625000 -0.00587133 1.01011
|
||||
1750000 -0.00867306 1.01495
|
||||
1875000 -0.0134768 1.02327
|
||||
2000000 -0.0229314 1.03995
|
||||
2125000 -0.0282333 1.04896
|
||||
2250000 -0.0202762 1.03477
|
||||
2375000 -0.0123279 1.02096
|
||||
2500000 -0.00546203 1.00923
|
||||
|
|
@ -0,0 +1,80 @@
|
|||
# created by fftool
|
||||
|
||||
print "Methane in TIP4P water"
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
read_data data.lmp
|
||||
|
||||
pair_style hybrid &
|
||||
lj/cut/coul/long 10.0 10.0 &
|
||||
lj/cut/tip4p/long/soft 3 4 2 2 0.125 1 0.5 10.0 10.0 10.0
|
||||
pair_modify tail no
|
||||
kspace_style pppm/tip4p 1.0e-4
|
||||
|
||||
pair_coeff 1 1 lj/cut/coul/long 0.0660 3.5000 # C4H C4H
|
||||
pair_coeff 1 2 lj/cut/coul/long 0.0445 2.9580 # C4H H
|
||||
pair_coeff 2 2 lj/cut/coul/long 0.0300 2.5000 # H H
|
||||
pair_coeff 3 3 lj/cut/tip4p/long/soft 0.1628 3.1644 1.0 # Ow Ow
|
||||
pair_coeff 3 4 lj/cut/tip4p/long/soft 0.0000 1.0000 1.0 # Ow Hw
|
||||
pair_coeff 4 4 lj/cut/tip4p/long/soft 0.0000 1.0000 1.0 # Hw Hw
|
||||
|
||||
pair_coeff 1 3 lj/cut/tip4p/long/soft 0.1036 3.3279 1.0 # C4H Ow
|
||||
pair_coeff 1 4 lj/cut/tip4p/long/soft 0.0000 1.0000 1.0 # C4H Hw
|
||||
pair_coeff 2 3 lj/cut/tip4p/long/soft 0.0699 2.8126 1.0 # H Ow
|
||||
pair_coeff 2 4 lj/cut/tip4p/long/soft 0.0000 1.0000 1.0 # H Hw
|
||||
|
||||
variable nsteps equal 2500000
|
||||
variable nprint equal ${nsteps}/500
|
||||
variable ndump equal ${nsteps}/100
|
||||
|
||||
variable temp equal 300.0
|
||||
variable press equal 1.0
|
||||
|
||||
fix fSHAKE all shake 0.0001 20 ${nprint} b 2 a 2
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
timestep 2.0
|
||||
|
||||
velocity all create ${temp} 12345
|
||||
|
||||
thermo_style multi
|
||||
thermo ${nprint}
|
||||
|
||||
fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 1000
|
||||
|
||||
run 250000
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
variable lambda equal ramp(1.0,0.0)
|
||||
|
||||
fix fADAPT all adapt/fep 125000 pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_lambda after yes
|
||||
|
||||
variable dlambda equal -0.002
|
||||
|
||||
compute cFEP all fep ${temp} pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_dlambda
|
||||
|
||||
fix fFEP all ave/time 25 4000 125000 c_cFEP[1] c_cFEP[2] file fdti10.lmp
|
||||
|
||||
# compute cRDF all rdf 100 3 3 3 4 4 4
|
||||
# fix fRDF all ave/time 2000 500 ${nsteps} c_cRDF file rdf.lammps mode vector
|
||||
|
||||
group owater type 3
|
||||
compute cMSD owater msd
|
||||
fix fMSD owater ave/time 1 1 ${ndump} c_cMSD[1] c_cMSD[2] c_cMSD[3] c_cMSD[4] file msd.lammps
|
||||
|
||||
dump dCONF all custom ${ndump} dump.lammpstrj id mol type element x y z ix iy iz
|
||||
dump_modify dCONF element C H O H
|
||||
|
||||
run ${nsteps}
|
||||
|
||||
# write_restart restart.*.lmp
|
||||
write_data data.*.lmp
|
||||
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,22 @@
|
|||
# Time-averaged data for fix fFEP
|
||||
# TimeStep c_cFEP[1] c_cFEP[2]
|
||||
125000 0.0806308 0.881044
|
||||
250000 0.251798 0.66945
|
||||
375000 0.448135 0.502774
|
||||
500000 0.670275 0.384034
|
||||
625000 0.873864 0.343148
|
||||
750000 0.689533 0.484145
|
||||
875000 0.474153 0.600305
|
||||
1000000 0.303566 0.740249
|
||||
1125000 0.165693 0.855143
|
||||
1250000 0.130949 0.88524
|
||||
1375000 0.0518948 0.976114
|
||||
1500000 0.0283335 1.0025
|
||||
1625000 -0.000790228 1.04259
|
||||
1750000 -0.0263791 1.0736
|
||||
1875000 -0.0587947 1.12568
|
||||
2000000 -0.0764999 1.15472
|
||||
2125000 -0.091264 1.17869
|
||||
2250000 -0.11294 1.21778
|
||||
2375000 -0.130721 1.25162
|
||||
2500000 -0.151808 1.29392
|
||||
|
|
@ -0,0 +1,80 @@
|
|||
# created by fftool
|
||||
|
||||
print "Methane in TIP4P water"
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
read_data data.lmp
|
||||
|
||||
pair_style hybrid &
|
||||
lj/cut/coul/long 10.0 10.0 &
|
||||
lj/cut/tip4p/long/soft 3 4 2 2 0.125 1 0.5 10.0 10.0 10.0
|
||||
pair_modify tail no
|
||||
kspace_style pppm/tip4p 1.0e-4
|
||||
|
||||
pair_coeff 1 1 lj/cut/coul/long 0.0660 3.5000 # C4H C4H
|
||||
pair_coeff 1 2 lj/cut/coul/long 0.0445 2.9580 # C4H H
|
||||
pair_coeff 2 2 lj/cut/coul/long 0.0300 2.5000 # H H
|
||||
pair_coeff 3 3 lj/cut/tip4p/long/soft 0.1628 3.1644 1.0 # Ow Ow
|
||||
pair_coeff 3 4 lj/cut/tip4p/long/soft 0.0000 1.0000 1.0 # Ow Hw
|
||||
pair_coeff 4 4 lj/cut/tip4p/long/soft 0.0000 1.0000 1.0 # Hw Hw
|
||||
|
||||
pair_coeff 1 3 lj/cut/tip4p/long/soft 0.1036 3.3279 0.0 # C4H Ow
|
||||
pair_coeff 1 4 lj/cut/tip4p/long/soft 0.0000 1.0000 0.0 # C4H Hw
|
||||
pair_coeff 2 3 lj/cut/tip4p/long/soft 0.0699 2.8126 0.0 # H Ow
|
||||
pair_coeff 2 4 lj/cut/tip4p/long/soft 0.0000 1.0000 0.0 # H Hw
|
||||
|
||||
variable nsteps equal 2500000
|
||||
variable nprint equal ${nsteps}/500
|
||||
variable ndump equal ${nsteps}/100
|
||||
|
||||
variable temp equal 300.0
|
||||
variable press equal 1.0
|
||||
|
||||
fix fSHAKE all shake 0.0001 20 ${nprint} b 2 a 2
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
timestep 2.0
|
||||
|
||||
velocity all create ${temp} 12345
|
||||
|
||||
thermo_style multi
|
||||
thermo ${nprint}
|
||||
|
||||
fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 1000
|
||||
|
||||
run 250000
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
variable lambda equal ramp(0.0,1.0)
|
||||
|
||||
fix fADAPT all adapt/fep 125000 pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_lambda after yes
|
||||
|
||||
variable dlambda equal 0.05
|
||||
|
||||
compute cFEP all fep ${temp} pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_dlambda
|
||||
|
||||
fix fFEP all ave/time 25 4000 125000 c_cFEP[1] c_cFEP[2] file fep01.lmp
|
||||
|
||||
# compute cRDF all rdf 100 3 3 3 4 4 4
|
||||
# fix fRDF all ave/time 2000 500 ${nsteps} c_cRDF file rdf.lammps mode vector
|
||||
|
||||
group owater type 3
|
||||
compute cMSD owater msd
|
||||
fix fMSD owater ave/time 1 1 ${ndump} c_cMSD[1] c_cMSD[2] c_cMSD[3] c_cMSD[4] file msd.lammps
|
||||
|
||||
dump dCONF all custom ${ndump} dump.lammpstrj id mol type element x y z ix iy iz
|
||||
dump_modify dCONF element C H O H
|
||||
|
||||
run ${nsteps}
|
||||
|
||||
# write_restart restart.*.lmp
|
||||
write_data data.*.lmp
|
||||
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,22 @@
|
|||
# Time-averaged data for fix fFEP
|
||||
# TimeStep c_cFEP[1] c_cFEP[2]
|
||||
125000 0.156203 0.771285
|
||||
250000 0.136448 0.799233
|
||||
375000 0.12198 0.820426
|
||||
500000 0.109453 0.840255
|
||||
625000 0.0921141 0.868102
|
||||
750000 0.0713015 0.905735
|
||||
875000 0.0622431 0.922352
|
||||
1000000 0.0330546 0.981942
|
||||
1125000 0.0197866 1.01134
|
||||
1250000 -0.00412826 1.06765
|
||||
1375000 -0.0174302 1.11343
|
||||
1500000 -0.0511646 1.18453
|
||||
1625000 -0.105676 1.36325
|
||||
1750000 -0.161616 1.56478
|
||||
1875000 -0.258263 1.93825
|
||||
2000000 -0.447487 3.0595
|
||||
2125000 -0.549377 3.01163
|
||||
2250000 -0.379009 2.01933
|
||||
2375000 -0.20934 1.45678
|
||||
2500000 -0.0644056 1.1252
|
||||
|
|
@ -0,0 +1,80 @@
|
|||
# created by fftool
|
||||
|
||||
print "Methane in TIP4P water"
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
read_data data.lmp
|
||||
|
||||
pair_style hybrid &
|
||||
lj/cut/coul/long 10.0 10.0 &
|
||||
lj/cut/tip4p/long/soft 3 4 2 2 0.125 1 0.5 10.0 10.0 10.0
|
||||
pair_modify tail no
|
||||
kspace_style pppm/tip4p 1.0e-4
|
||||
|
||||
pair_coeff 1 1 lj/cut/coul/long 0.0660 3.5000 # C4H C4H
|
||||
pair_coeff 1 2 lj/cut/coul/long 0.0445 2.9580 # C4H H
|
||||
pair_coeff 2 2 lj/cut/coul/long 0.0300 2.5000 # H H
|
||||
pair_coeff 3 3 lj/cut/tip4p/long/soft 0.1628 3.1644 1.0 # Ow Ow
|
||||
pair_coeff 3 4 lj/cut/tip4p/long/soft 0.0000 1.0000 1.0 # Ow Hw
|
||||
pair_coeff 4 4 lj/cut/tip4p/long/soft 0.0000 1.0000 1.0 # Hw Hw
|
||||
|
||||
pair_coeff 1 3 lj/cut/tip4p/long/soft 0.1036 3.3279 1.0 # C4H Ow
|
||||
pair_coeff 1 4 lj/cut/tip4p/long/soft 0.0000 1.0000 1.0 # C4H Hw
|
||||
pair_coeff 2 3 lj/cut/tip4p/long/soft 0.0699 2.8126 1.0 # H Ow
|
||||
pair_coeff 2 4 lj/cut/tip4p/long/soft 0.0000 1.0000 1.0 # H Hw
|
||||
|
||||
variable nsteps equal 2500000
|
||||
variable nprint equal ${nsteps}/500
|
||||
variable ndump equal ${nsteps}/100
|
||||
|
||||
variable temp equal 300.0
|
||||
variable press equal 1.0
|
||||
|
||||
fix fSHAKE all shake 0.0001 20 ${nprint} b 2 a 2
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
timestep 2.0
|
||||
|
||||
velocity all create ${temp} 12345
|
||||
|
||||
thermo_style multi
|
||||
thermo ${nprint}
|
||||
|
||||
fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 1000
|
||||
|
||||
run 250000
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
variable lambda equal ramp(1.0,0.0)
|
||||
|
||||
fix fADAPT all adapt/fep 125000 pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_lambda after yes
|
||||
|
||||
variable dlambda equal -0.05
|
||||
|
||||
compute cFEP all fep ${temp} pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_dlambda
|
||||
|
||||
fix fFEP all ave/time 25 4000 125000 c_cFEP[1] c_cFEP[2] file fep10.lmp
|
||||
|
||||
# compute cRDF all rdf 100 3 3 3 4 4 4
|
||||
# fix fRDF all ave/time 2000 500 ${nsteps} c_cRDF file rdf.lammps mode vector
|
||||
|
||||
group owater type 3
|
||||
compute cMSD owater msd
|
||||
fix fMSD owater ave/time 1 1 ${ndump} c_cMSD[1] c_cMSD[2] c_cMSD[3] c_cMSD[4] file msd.lammps
|
||||
|
||||
dump dCONF all custom ${ndump} dump.lammpstrj id mol type element x y z ix iy iz
|
||||
dump_modify dCONF element C H O H
|
||||
|
||||
run ${nsteps}
|
||||
|
||||
# write_restart restart.*.lmp
|
||||
write_data data.*.lmp
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,9 @@
|
|||
methane
|
||||
|
||||
1 C4H
|
||||
2 H 1 1.09
|
||||
3 H 1 1.09 2 109.5
|
||||
4 H 1 1.09 2 109.5 3 120.0
|
||||
5 H 1 1.09 2 109.5 3 -120.0
|
||||
|
||||
oplsaa.ff
|
||||
|
|
@ -0,0 +1,85 @@
|
|||
# oplsaa.ff (kJ/mol, A, deg) version 2013/07/27
|
||||
|
||||
ATOMS
|
||||
# type m/uma q/e pot pars
|
||||
# alkanes OPLS-AA JACS 118(1996)11225, JPC 100(1996)18010
|
||||
C4C CT 12.011 0.00 lj 3.50 0.27614
|
||||
C4H CT 4.011 -0.24 lj 3.50 0.27614
|
||||
C3H CT 12.011 -0.18 lj 3.50 0.27614
|
||||
C2H CT 12.011 -0.12 lj 3.50 0.27614
|
||||
H HC 4.008 0.06 lj 2.50 0.12552
|
||||
# alcohols OPLS-AA JACS 118(1996)11225, JPC 100(1996)18010
|
||||
CTO CT 12.011 0.145 lj 3.50 0.27614
|
||||
CET CT 12.011 -0.140 lj 3.50 0.27614
|
||||
C2T CT 12.011 -0.080 lj 3.50 0.27614
|
||||
H1O HC 1.008 0.040 lj 2.50 0.12552
|
||||
OH OH 15.999 -0.683 lj 3.12 0.71128
|
||||
HO HO 1.008 0.418 lj 0.00 0.00000
|
||||
# aromatics OPLS-AA JACS 118(1996)11225
|
||||
CA CA 12.011 -0.115 lj 3.55 0.43932
|
||||
HA HA 1.008 0.115 lj 2.42 0.12552
|
||||
# toluene OPLS-AA JACS 118(1996)11217, JCC 25(2004)1322
|
||||
CAP CA 12.011 -0.154 lj 3.55 0.43932
|
||||
CAM CA 12.011 -0.145 lj 3.55 0.43932
|
||||
CAO CA 12.011 -0.147 lj 3.55 0.43932
|
||||
CAT CA 12.011 -0.081 lj 3.55 0.43932
|
||||
CTT CT 12.011 -0.197 lj 3.50 0.27614
|
||||
HAT HA 1.008 0.148 lj 2.42 0.12552
|
||||
HT HC 1.008 0.092 lj 2.42 0.12552
|
||||
|
||||
BONDS
|
||||
# i j pot re/A ka/kJmol-1
|
||||
# alkanes OPLS-AA JACS 118(1996)11225, JPC 100(1996)18010
|
||||
HC CT harm 1.090 2845.12
|
||||
CT CT harm 1.529 2242.62
|
||||
# alcohols OPLS-AA JACS 118(1996)11225, JPC 100(1996)18010
|
||||
CT OH harm 1.410 2677.76
|
||||
HO OH cons 0.945 4627.50
|
||||
# aromatics AMBER JACS 117(1995)5179
|
||||
CA CA harm 1.400 3924.6
|
||||
CA HA cons 1.080 3071.1
|
||||
# toluene AMBER JACS 117(1995)5179
|
||||
CA CT harm 1.510 2652.7
|
||||
|
||||
ANGLES
|
||||
# i j k pot th/deg ka/kjmol-1
|
||||
# alkanes OPLS-AA JACS 118(1996)11225, JPC 100(1996)18010
|
||||
HC CT HC harm 107.80 276.14
|
||||
HC CT CT harm 110.70 313.80
|
||||
CT CT CT harm 112.70 488.27
|
||||
# alcohols OPLS-AA JACS 118(1996)11225, JPC 100(1996)18010
|
||||
CT CT OH harm 109.50 418.40
|
||||
HC CT OH harm 109.50 292.88
|
||||
CT OH HO harm 108.50 460.24
|
||||
# aromatics AMBER JACS 117(1995)5179
|
||||
CA CA HA harm 120.00 292.88
|
||||
CA CA CA harm 120.00 527.18
|
||||
# toluene AMBER JACS 117(1995)5179
|
||||
CA CA CT harm 120.00 585.76
|
||||
CA CT HC harm 109.50 418.4
|
||||
|
||||
DIHEDRALS
|
||||
# i j k l pot v1 v2 v3 v4
|
||||
# alkanes OPLS-AA JACS 118: 11225 (1996); J Phys Chem 100: 18010 (1996)
|
||||
HC CT CT HC opls 0.0000 0.0000 1.3305 0.0000
|
||||
HC CT CT CT opls 0.0000 0.0000 1.5313 0.0000
|
||||
CT CT CT CT opls 7.2800 -0.6569 1.1673 0.0000
|
||||
# alcohols OPLS-AA JACS 118(1996)11225, AMBER98 (OCCO) 117(1995)5179
|
||||
HC CT OH HO opls 0.0000 0.0000 1.8828 0.0000
|
||||
CT CT OH HO opls -1.4895 -0.7280 2.0585 0.0000
|
||||
HC CT CT OH opls 0.0000 0.0000 1.9581 0.0000
|
||||
OH CT CT OH opls 0.0000 -9.8324 1.2050 0.0000
|
||||
# aromatics AMBER JACS 117(1995)5179
|
||||
CA CA CA CA opls 0.0000 30.334 0.0000 0.0000
|
||||
CA CA CA HA opls 0.0000 30.334 0.0000 0.0000
|
||||
HA CA CA HA opls 0.0000 30.334 0.0000 0.0000
|
||||
# toluene AMBER JACS 117: 5179 (1995)
|
||||
CT CA CA CA opls 0.0000 30.334 0.0000 0.0000
|
||||
CT CA CA HA opls 0.0000 30.334 0.0000 0.0000
|
||||
CA CA CT HC opls 0.0000 0.0000 0.0000 0.0000
|
||||
|
||||
IMPROPER
|
||||
# improper aromatics AMBER JACS 117(1995)5179
|
||||
CA CA CA HA opls 0.0000 9.2048 0.0000 0.0000
|
||||
# improper toluene AMBER JACS 117: 5179 (1995)
|
||||
CA CA CA CT opls 0.0000 9.2048 0.0000 0.0000
|
||||
|
|
@ -0,0 +1,14 @@
|
|||
# TIP4P-Ew water (kJ/mol, A, deg)
|
||||
|
||||
ATOMS
|
||||
# type m/uma q/e pot pars
|
||||
Ow Ow 15.999 -1.04844 lj 3.16435 0.680946
|
||||
Hw Hw 1.008 0.52422 lj 0.00000 0.000000
|
||||
|
||||
BONDS
|
||||
# i j pot re/A ka/kJmol-1
|
||||
Ow Hw cons 0.9572 4331.53
|
||||
|
||||
ANGLES
|
||||
# i j k pot th/deg ka/kjmol-1
|
||||
Hw Ow Hw cons 104.52 317.57
|
||||
|
|
@ -0,0 +1,7 @@
|
|||
TIP4P-Ew
|
||||
|
||||
Ow
|
||||
Hw 1 0.9572
|
||||
Hw 1 0.9572 2 104.52
|
||||
|
||||
tip4pew.ff
|
||||
|
|
@ -0,0 +1,11 @@
|
|||
compute fep examples
|
||||
====================
|
||||
|
||||
* `CH4hyd` -- free energy of hydration of methane (very simple). FEP
|
||||
and TI methods.
|
||||
|
||||
* `CH4-CF4` -- free energy difference of transforming methane into
|
||||
perfluoromethane, in water (simple). BAR method.
|
||||
|
||||
* `CC-CO` -- free energy difference of transforming ethane into
|
||||
methanol, in water (more complex). FEP, TI and BAR methods.
|
||||
Loading…
Reference in New Issue