forked from lijiext/lammps
58 lines
2.4 KiB
Plaintext
58 lines
2.4 KiB
Plaintext
Methane to Tetrafluoromethane 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 methane into tetrafluoromethane with LAMMPS using
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*compute fep* and *fix adapt*.
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Methane and tetrafluoromethane are represented by the OPLS-AA force
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field (1 molecule). Water is represented by the 3-site SPC/E model
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(360 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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methane and perfluorommethane are present throughout the simulation,
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only some 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 Bennet's acceptance ratio (BAR) method:
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* `bar01` -- Calculation using BAR, 1-step transformation of a CH4
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molecule into CF4. Results in `bar01.lmp`
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* `bar10` -- Calculation using BAR, 1-step transformation of a
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CF4 molecule into CH4. Results in `bar10.lmp`
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The Python script `bar.py` found in the `tools` directory can
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be used to calculate the free-energy difference corresponding to the
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transformation:
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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 1.2 kcal/mol and with a simulation value from the literature
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(using a different force field): 0.8 kcal/mol
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[Gough, Pearlman, Kolmann, J Chem Phys 99 (1993) 9103]. This small
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free energy difference is difficult to predict.
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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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