forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8163 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
1cfdda1f82
commit
44904c5bf3
File diff suppressed because it is too large
Load Diff
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@ -0,0 +1,48 @@
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# Solvated 5-mer peptide
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units real
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atom_style full
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pair_style lj/charmm/coul/long 8.0 10.0 10.0
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bond_style harmonic
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angle_style charmm
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dihedral_style charmm
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improper_style harmonic
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kspace_style pppm 0.0001
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read_data data.peptide
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neighbor 2.0 bin
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neigh_modify delay 5
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timestep 2.0
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group peptide type <= 12
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group one id 2 4 5 6
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group two id 80 82 83 84
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group ref id 37
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group colvar union one two ref
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fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
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shell "rm -f out*.colvars.*"
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fix 2 all colvars peptide.colvars
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fix 2a ref setforce 0.0 0.0 0.0
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fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
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#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
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#dump_modify 1 sort id
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thermo_style custom step temp etotal pe ke epair ebond f_2
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thermo 10
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run 100
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run 100
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fix 2 all colvars peptide.colvars input out.colvars.state output out2
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run 100
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@ -0,0 +1,40 @@
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# Solvated 5-mer peptide
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units real
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atom_style full
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pair_style lj/charmm/coul/long 8.0 10.0 10.0
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bond_style harmonic
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angle_style charmm
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dihedral_style charmm
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improper_style harmonic
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kspace_style pppm 0.0001
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read_data data.peptide
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neighbor 2.0 bin
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neigh_modify delay 5
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timestep 2.0
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group peptide type <= 12
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group one id 2 4 5 6
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group two id 80 82 83 84
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group ref id 37
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group colvar union one two ref
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fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
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shell "rm -f peptide2.colvars.*"
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fix 2 all colvars peptide.colvars2 output peptide2
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fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
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#dump 1 colvar custom 1 dump.colvar2.lammpstrj id xu yu zu fx fy fz
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#dump_modify 1 sort id
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thermo_style custom step temp etotal pe ke epair ebond f_2
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thermo 10
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run 100
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@ -0,0 +1,516 @@
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LAMMPS (21 May 2012-ICMS)
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# Solvated 5-mer peptide
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units real
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atom_style full
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pair_style lj/charmm/coul/long 8.0 10.0 10.0
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bond_style harmonic
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angle_style charmm
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dihedral_style charmm
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improper_style harmonic
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kspace_style pppm 0.0001
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read_data data.peptide
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3 = max bonds/atom
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6 = max angles/atom
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14 = max dihedrals/atom
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1 = max impropers/atom
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orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
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1 by 1 by 1 MPI processor grid
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2004 atoms
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2004 velocities
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1365 bonds
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786 angles
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207 dihedrals
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12 impropers
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4 = max # of 1-2 neighbors
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7 = max # of 1-3 neighbors
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14 = max # of 1-4 neighbors
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18 = max # of special neighbors
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neighbor 2.0 bin
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neigh_modify delay 5
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timestep 2.0
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group peptide type <= 12
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84 atoms in group peptide
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group one id 2 4 5 6
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4 atoms in group one
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group two id 80 82 83 84
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4 atoms in group two
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group ref id 37
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1 atoms in group ref
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group colvar union one two ref
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9 atoms in group colvar
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fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
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shell "rm -f out*.colvars.*"
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fix 2 all colvars peptide.colvars
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fix 2a ref setforce 0.0 0.0 0.0
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fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
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19 = # of size 2 clusters
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6 = # of size 3 clusters
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3 = # of size 4 clusters
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640 = # of frozen angles
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#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
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#dump_modify 1 sort id
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thermo_style custom step temp etotal pe ke epair ebond f_2
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thermo 10
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run 100
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PPPM initialization ...
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G vector (1/distance) = 0.268721
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grid = 15 15 15
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stencil order = 5
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estimated absolute RMS force accuracy = 0.01614
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estimated relative force accuracy = 4.86052e-05
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using single precision FFTs
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brick FFT buffer size/proc = 10648 3375 5808
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colvars: ----------------------------------------------------------------------
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colvars: Initializing the collective variables module, version 2012-03-23.
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colvars: # analysis = off [default]
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colvars: # colvarsTrajFrequency = 1
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colvars: # colvarsRestartFrequency = 1000
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colvars: # colvarsTrajAppend = off [default]
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colvars: The restart output state file will be "rest.colvars.state".
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colvars: The final output state file will be "out.colvars.state".
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colvars: The trajectory file will be "out.colvars.traj".
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colvars: ----------------------------------------------------------------------
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colvars: Initializing a new collective variable.
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colvars: # name = one
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colvars: Initializing a new "distance" component.
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colvars: # componentCoeff = 1 [default]
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colvars: # componentExp = 1 [default]
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colvars: # period = 0 [default]
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colvars: # wrapAround = 0 [default]
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colvars: # forceNoPBC = off [default]
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colvars: # oneSiteSystemForce = off [default]
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colvars: Initializing atom group "group1".
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colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
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colvars: Initializing atom group "group2".
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colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
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colvars: All components initialized.
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colvars: # width = 1 [default]
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colvars: # lowerBoundary = 0 [default]
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colvars: # lowerWallConstant = 0 [default]
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colvars: # upperBoundary = 0 [default]
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colvars: # upperWallConstant = 0 [default]
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colvars: # expandBoundaries = off [default]
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colvars: # extendedLagrangian = off [default]
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colvars: # outputValue = on [default]
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colvars: # outputVelocity = off [default]
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colvars: # outputSystemForce = off [default]
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colvars: # outputAppliedForce = off [default]
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colvars: ----------------------------------------------------------------------
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colvars: Initializing a new collective variable.
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colvars: # name = two
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colvars: Initializing a new "distance" component.
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colvars: # componentCoeff = 1 [default]
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colvars: # componentExp = 1 [default]
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colvars: # period = 0 [default]
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colvars: # wrapAround = 0 [default]
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colvars: # forceNoPBC = off [default]
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colvars: # oneSiteSystemForce = off [default]
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colvars: Initializing atom group "group1".
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colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
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colvars: Initializing atom group "group2".
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colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
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colvars: All components initialized.
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colvars: # width = 1 [default]
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colvars: # lowerBoundary = 0 [default]
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colvars: # lowerWallConstant = 0 [default]
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colvars: # upperBoundary = 0 [default]
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colvars: # upperWallConstant = 0 [default]
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colvars: # expandBoundaries = off [default]
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colvars: # extendedLagrangian = off [default]
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colvars: # outputValue = on [default]
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colvars: # outputVelocity = off [default]
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colvars: # outputSystemForce = off [default]
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colvars: # outputAppliedForce = off [default]
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colvars: ----------------------------------------------------------------------
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colvars: Collective variables initialized, 2 in total.
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colvars: ----------------------------------------------------------------------
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colvars: Initializing a new "harmonic" instance.
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colvars: # name = h_pot
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colvars: # colvars = { one, two }
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colvars: # forceConstant = 100
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colvars: # centers = { 10, 10 }
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colvars: # targetCenters = { 10, 10 } [default]
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colvars: # targetForceConstant = 0 [default]
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colvars: ----------------------------------------------------------------------
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colvars: Collective variables biases initialized, 1 in total.
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colvars: ----------------------------------------------------------------------
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colvars: Collective variables module initialized.
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colvars: ----------------------------------------------------------------------
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SHAKE stats (type/ave/delta) on step 0
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4 1.111 1.44264e-05
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6 0.996998 7.26967e-06
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8 1.08 1.32536e-05
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10 1.111 1.22749e-05
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12 1.08 1.11767e-05
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14 0.96 0
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18 0.957206 4.37979e-05
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31 104.519 0.00396029
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Memory usage per processor = 22.5866 Mbytes
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Step Temp TotEng PotEng KinEng E_pair E_bond 2
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0 282.10052 -5237.458 -6372.3765 1134.9186 -6442.7679 16.557152 292.14604
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10 305.06198 -5058.8899 -6286.1847 1227.2948 -6413.0967 58.849896 103.38344
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20 311.00592 -4999.0544 -6250.2623 1251.2079 -6417.0984 47.695274 36.699706
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30 314.22398 -4993.6953 -6257.8498 1264.1545 -6421.9643 35.344163 10.563914
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40 297.87524 -5020.8339 -6219.2158 1198.3819 -6389.8501 27.723201 3.8354392
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50 304.02086 -5056.2539 -6279.3602 1223.1063 -6456.8181 55.459508 0.20679801
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60 285.92594 -5104.0436 -6254.3523 1150.3086 -6435.5793 32.76729 0.69356508
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70 277.835 -5163.9752 -6281.7332 1117.758 -6447.7015 39.627148 11.433632
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80 267.51473 -5206.4042 -6282.6427 1076.2385 -6456.6352 31.611843 6.3553235
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90 278.15513 -5245.383 -6364.4289 1119.0459 -6499.8037 28.849899 0.36938867
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SHAKE stats (type/ave/delta) on step 100
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4 1.11098 8.97184e-05
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6 0.996996 1.00568e-05
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8 1.08 6.02345e-06
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10 1.111 1.84257e-05
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12 1.08 7.27136e-06
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14 0.959996 0
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18 0.957198 3.36077e-05
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31 104.52 0.00306008
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100 260.10505 -5292.6892 -6339.1178 1046.4286 -6471.6694 25.361885 0.2198687
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colvars: Saving collective variables state to "out.colvars.state".
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Loop time of 2.39102 on 1 procs for 100 steps with 2004 atoms
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Pair time (%) = 1.86583 (78.0347)
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Bond time (%) = 0.00628591 (0.262896)
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Kspace time (%) = 0.165128 (6.90614)
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Neigh time (%) = 0.314792 (13.1656)
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Comm time (%) = 0.0111108 (0.464687)
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Output time (%) = 0.000252724 (0.0105697)
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Modify time (%) = 0.0253747 (1.06125)
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Other time (%) = 0.0022521 (0.0941899)
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FFT time (% of Kspce) = 0.0274372 (16.6158)
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FFT Gflps 3d (1d only) = 1.99867 2.86506
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Nlocal: 2004 ave 2004 max 2004 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 11124 ave 11124 max 11124 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 708237 ave 708237 max 708237 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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|
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Total # of neighbors = 708237
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Ave neighs/atom = 353.412
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Ave special neighs/atom = 2.34032
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Neighbor list builds = 12
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Dangerous builds = 2
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|
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run 100
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PPPM initialization ...
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G vector (1/distance) = 0.268721
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grid = 15 15 15
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stencil order = 5
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||||
estimated absolute RMS force accuracy = 0.01614
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estimated relative force accuracy = 4.86052e-05
|
||||
using single precision FFTs
|
||||
brick FFT buffer size/proc = 10648 3375 5808
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colvars: ----------------------------------------------------------------------
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||||
colvars: Initializing the collective variables module, version 2012-03-23.
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colvars: # analysis = off [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # colvarsTrajAppend = off [default]
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "out.colvars.state".
|
||||
colvars: The trajectory file will be "out.colvars.traj".
|
||||
colvars: ----------------------------------------------------------------------
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||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = one
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
|
||||
colvars: All components initialized.
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # lowerWallConstant = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # upperWallConstant = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputSystemForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = two
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
|
||||
colvars: All components initialized.
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # lowerWallConstant = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # upperWallConstant = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputSystemForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 2 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = h_pot
|
||||
colvars: # colvars = { one, two }
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # centers = { 10, 10 }
|
||||
colvars: # targetCenters = { 10, 10 } [default]
|
||||
colvars: # targetForceConstant = 0 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Restarting from file "out.colvars.state".
|
||||
colvars: Restarting collective variable "one" from value: 10.0137
|
||||
colvars: Restarting collective variable "two" from value: 10.0649
|
||||
colvars: Restarting harmonic bias "h_pot".
|
||||
colvars: Reading current stage from the restart.
|
||||
colvars: # stage = 3900175693153042431
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing step number as firstTimestep.
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11098 8.97184e-05
|
||||
6 0.996996 1.00568e-05
|
||||
8 1.08 6.02345e-06
|
||||
10 1.111 1.84257e-05
|
||||
12 1.08 7.27136e-06
|
||||
14 0.959996 0
|
||||
18 0.957198 3.36077e-05
|
||||
31 104.52 0.00306008
|
||||
Memory usage per processor = 22.5866 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond 2
|
||||
100 260.10505 -5292.6892 -6339.1178 1046.4286 -6471.6694 25.361885 0.2198687
|
||||
110 266.26278 -5341.2103 -6412.412 1071.2018 -6552.7583 33.572968 1.9229782
|
||||
120 262.66442 -5386.2494 -6442.9746 1056.7252 -6587.5499 29.859553 2.7124877
|
||||
130 252.8344 -5422.5446 -6439.7226 1017.1781 -6580.4752 25.979049 1.2031628
|
||||
140 253.85115 -5452.1905 -6473.4591 1021.2686 -6609.489 26.071514 0.30586247
|
||||
150 261.31825 -5490.48 -6541.7895 1051.3095 -6646.6144 16.258548 6.9049974
|
||||
160 255.7368 -5521.6048 -6550.4596 1028.8547 -6658.1517 19.717533 12.339821
|
||||
170 253.42877 -5540.1003 -6559.6695 1019.5693 -6656.6878 23.293662 10.289878
|
||||
180 248.51086 -5550.3244 -6550.1084 999.78404 -6661.4182 26.200056 3.4339065
|
||||
190 250.8039 -5555.2614 -6564.2706 1009.0092 -6666.15 25.536594 3.3495152
|
||||
SHAKE stats (type/ave/delta) on step 200
|
||||
4 1.111 1.8129e-06
|
||||
6 0.997 7.7964e-07
|
||||
8 1.08 1.08934e-06
|
||||
10 1.111 2.96501e-07
|
||||
12 1.08 4.69174e-07
|
||||
14 0.960001 0
|
||||
18 0.957201 3.76571e-06
|
||||
31 104.52 0.000411068
|
||||
200 251.50581 -5557.4209 -6569.2539 1011.833 -6674.0867 24.805164 7.1388858
|
||||
colvars: Saving collective variables state to "out.colvars.state".
|
||||
Loop time of 2.23495 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Pair time (%) = 1.84544 (82.572)
|
||||
Bond time (%) = 0.00609159 (0.27256)
|
||||
Kspace time (%) = 0.163201 (7.30223)
|
||||
Neigh time (%) = 0.183405 (8.20622)
|
||||
Comm time (%) = 0.00959301 (0.429227)
|
||||
Output time (%) = 0.000245094 (0.0109664)
|
||||
Modify time (%) = 0.0247326 (1.10663)
|
||||
Other time (%) = 0.00223875 (0.10017)
|
||||
|
||||
FFT time (% of Kspce) = 0.0272989 (16.7271)
|
||||
FFT Gflps 3d (1d only) = 2.0088 2.93901
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11159 ave 11159 max 11159 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708088 ave 708088 max 708088 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708088
|
||||
Ave neighs/atom = 353.337
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 7
|
||||
Dangerous builds = 0
|
||||
|
||||
fix 2 all colvars peptide.colvars input out.colvars.state output out2
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.268721
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.01614
|
||||
estimated relative force accuracy = 4.86052e-05
|
||||
using single precision FFTs
|
||||
brick FFT buffer size/proc = 10648 3375 5808
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2012-03-23.
|
||||
colvars: # analysis = off [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # colvarsTrajAppend = off [default]
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "out2.colvars.state".
|
||||
colvars: The trajectory file will be "out2.colvars.traj".
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = one
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
|
||||
colvars: All components initialized.
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # lowerWallConstant = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # upperWallConstant = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputSystemForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = two
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
|
||||
colvars: All components initialized.
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # lowerWallConstant = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # upperWallConstant = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputSystemForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 2 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = h_pot
|
||||
colvars: # colvars = { one, two }
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # centers = { 10, 10 }
|
||||
colvars: # targetCenters = { 10, 10 } [default]
|
||||
colvars: # targetForceConstant = 0 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Restarting from file "out.colvars.state".
|
||||
colvars: Restarting collective variable "one" from value: 10.0128
|
||||
colvars: Restarting collective variable "two" from value: 9.62236
|
||||
colvars: Restarting harmonic bias "h_pot".
|
||||
colvars: Reading current stage from the restart.
|
||||
colvars: # stage = 3900175693153042431
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing step number as firstTimestep.
|
||||
SHAKE stats (type/ave/delta) on step 200
|
||||
4 1.111 1.8129e-06
|
||||
6 0.997 7.7964e-07
|
||||
8 1.08 1.08934e-06
|
||||
10 1.111 2.96501e-07
|
||||
12 1.08 4.69174e-07
|
||||
14 0.960001 0
|
||||
18 0.957201 3.76571e-06
|
||||
31 104.52 0.000411068
|
||||
Memory usage per processor = 22.5866 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond 2
|
||||
200 251.50581 -5557.4209 -6569.2539 1011.833 -6674.0867 24.805164 7.1388858
|
||||
210 253.15043 -5538.5668 -6557.0163 1018.4495 -6672.041 37.67158 0.61296982
|
||||
220 245.19746 -5522.5242 -6508.9781 986.4539 -6628.1999 36.656356 0.048624555
|
||||
230 258.65299 -5495.7177 -6536.3046 1040.5868 -6658.0952 34.855726 0.22046598
|
||||
240 260.80143 -5469.8517 -6519.0819 1049.2302 -6624.1723 31.576409 3.7570726
|
||||
250 269.06507 -5438.3971 -6520.8727 1082.4757 -6616.3871 25.444125 8.6640978
|
||||
260 266.10282 -5397.3162 -6467.8744 1070.5583 -6580.628 26.873936 8.3330854
|
||||
270 272.81993 -5350.8393 -6448.4211 1097.5819 -6563.8139 23.113421 10.972906
|
||||
280 279.52079 -5307.9855 -6432.5256 1124.5401 -6557.7274 33.641095 8.5474821
|
||||
290 286.81184 -5260.8728 -6414.7455 1153.8727 -6515.5418 28.572468 5.9092648
|
||||
SHAKE stats (type/ave/delta) on step 300
|
||||
4 1.111 1.79733e-05
|
||||
6 0.997005 1.02622e-05
|
||||
8 1.08 1.84996e-05
|
||||
10 1.111 9.98595e-06
|
||||
12 1.08 8.83195e-06
|
||||
14 0.960008 0
|
||||
18 0.957203 1.84801e-05
|
||||
31 104.52 0.00169221
|
||||
300 291.51842 -5216.3285 -6389.1362 1172.8077 -6503.1141 27.877464 2.2482411
|
||||
colvars: Saving collective variables state to "out2.colvars.state".
|
||||
Loop time of 2.25031 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Pair time (%) = 1.83745 (81.6533)
|
||||
Bond time (%) = 0.00609803 (0.270987)
|
||||
Kspace time (%) = 0.162178 (7.20694)
|
||||
Neigh time (%) = 0.207886 (9.23812)
|
||||
Comm time (%) = 0.00977254 (0.434276)
|
||||
Output time (%) = 0.000240803 (0.0107009)
|
||||
Modify time (%) = 0.024461 (1.08701)
|
||||
Other time (%) = 0.00221944 (0.0986283)
|
||||
|
||||
FFT time (% of Kspce) = 0.0273609 (16.8709)
|
||||
FFT Gflps 3d (1d only) = 2.00425 2.94806
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11292 ave 11292 max 11292 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708145 ave 708145 max 708145 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708145
|
||||
Ave neighs/atom = 353.366
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 8
|
||||
Dangerous builds = 0
|
||||
|
||||
|
|
@ -0,0 +1,516 @@
|
|||
LAMMPS (21 May 2012-ICMS)
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
3 = max bonds/atom
|
||||
6 = max angles/atom
|
||||
14 = max dihedrals/atom
|
||||
1 = max impropers/atom
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
2004 atoms
|
||||
2004 velocities
|
||||
1365 bonds
|
||||
786 angles
|
||||
207 dihedrals
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
shell "rm -f out*.colvars.*"
|
||||
fix 2 all colvars peptide.colvars
|
||||
fix 2a ref setforce 0.0 0.0 0.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
|
||||
#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_2
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.268721
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.01614
|
||||
estimated relative force accuracy = 4.86052e-05
|
||||
using single precision FFTs
|
||||
brick FFT buffer size/proc = 4312 960 3696
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2012-03-23.
|
||||
colvars: # analysis = off [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # colvarsTrajAppend = off [default]
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "out.colvars.state".
|
||||
colvars: The trajectory file will be "out.colvars.traj".
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = one
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
|
||||
colvars: All components initialized.
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # lowerWallConstant = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # upperWallConstant = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputSystemForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = two
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
|
||||
colvars: All components initialized.
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # lowerWallConstant = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # upperWallConstant = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputSystemForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 2 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = h_pot
|
||||
colvars: # colvars = { one, two }
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # centers = { 10, 10 }
|
||||
colvars: # targetCenters = { 10, 10 } [default]
|
||||
colvars: # targetForceConstant = 0 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Memory usage per processor = 10.1924 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond 2
|
||||
0 282.10052 -5237.458 -6372.3765 1134.9186 -6442.7679 16.557152 292.14604
|
||||
10 305.06198 -5058.8898 -6286.1847 1227.2948 -6413.0967 58.849896 103.38344
|
||||
20 311.00592 -4999.0545 -6250.2624 1251.2079 -6417.0984 47.695274 36.699706
|
||||
30 314.22398 -4993.6953 -6257.8498 1264.1545 -6421.9643 35.344162 10.563914
|
||||
40 297.87524 -5020.8339 -6219.2157 1198.3819 -6389.85 27.723201 3.8354392
|
||||
50 304.02086 -5056.254 -6279.3603 1223.1063 -6456.8182 55.459508 0.206798
|
||||
60 285.92594 -5104.0436 -6254.3523 1150.3086 -6435.5793 32.767289 0.69356507
|
||||
70 277.835 -5163.9751 -6281.7331 1117.758 -6447.7014 39.627147 11.433632
|
||||
80 267.51474 -5206.4042 -6282.6428 1076.2385 -6456.6352 31.611843 6.3553237
|
||||
90 278.15513 -5245.383 -6364.4289 1119.0459 -6499.8036 28.849898 0.36938879
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11098 8.97184e-05
|
||||
6 0.996996 1.00568e-05
|
||||
8 1.08 6.02345e-06
|
||||
10 1.111 1.84257e-05
|
||||
12 1.08 7.27136e-06
|
||||
14 0.959996 0
|
||||
18 0.957198 3.36077e-05
|
||||
31 104.52 0.00306008
|
||||
100 260.10504 -5292.6891 -6339.1176 1046.4286 -6471.6693 25.361886 0.21986866
|
||||
colvars: Saving collective variables state to "out.colvars.state".
|
||||
Loop time of 0.686681 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Pair time (%) = 0.47104 (68.5966)
|
||||
Bond time (%) = 0.00184608 (0.26884)
|
||||
Kspace time (%) = 0.0808357 (11.7719)
|
||||
Neigh time (%) = 0.0772016 (11.2427)
|
||||
Comm time (%) = 0.0293136 (4.26888)
|
||||
Output time (%) = 0.000323951 (0.0471764)
|
||||
Modify time (%) = 0.0247293 (3.60128)
|
||||
Other time (%) = 0.00139064 (0.202516)
|
||||
|
||||
FFT time (% of Kspce) = 0.0117171 (14.4949)
|
||||
FFT Gflps 3d (1d only) = 4.68018 10.009
|
||||
|
||||
Nlocal: 501 ave 513 max 489 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Nghost: 6563.25 ave 6596 max 6519 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 177059 ave 181741 max 172943 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 708237
|
||||
Ave neighs/atom = 353.412
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 2
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.268721
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.01614
|
||||
estimated relative force accuracy = 4.86052e-05
|
||||
using single precision FFTs
|
||||
brick FFT buffer size/proc = 4312 960 3696
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2012-03-23.
|
||||
colvars: # analysis = off [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # colvarsTrajAppend = off [default]
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "out.colvars.state".
|
||||
colvars: The trajectory file will be "out.colvars.traj".
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = one
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
|
||||
colvars: All components initialized.
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # lowerWallConstant = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # upperWallConstant = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputSystemForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = two
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
|
||||
colvars: All components initialized.
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # lowerWallConstant = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # upperWallConstant = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputSystemForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 2 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = h_pot
|
||||
colvars: # colvars = { one, two }
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # centers = { 10, 10 }
|
||||
colvars: # targetCenters = { 10, 10 } [default]
|
||||
colvars: # targetForceConstant = 0 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Restarting from file "out.colvars.state".
|
||||
colvars: Restarting collective variable "one" from value: 10.0137
|
||||
colvars: Restarting collective variable "two" from value: 10.0649
|
||||
colvars: Restarting harmonic bias "h_pot".
|
||||
colvars: Reading current stage from the restart.
|
||||
colvars: # stage = 8103505641670189088
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing step number as firstTimestep.
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11098 8.97184e-05
|
||||
6 0.996996 1.00568e-05
|
||||
8 1.08 6.02345e-06
|
||||
10 1.111 1.84257e-05
|
||||
12 1.08 7.27136e-06
|
||||
14 0.959996 0
|
||||
18 0.957198 3.36077e-05
|
||||
31 104.52 0.00306008
|
||||
Memory usage per processor = 10.1967 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond 2
|
||||
100 260.10504 -5292.6891 -6339.1176 1046.4286 -6471.6693 25.361886 0.21986866
|
||||
110 266.26278 -5341.2101 -6412.4119 1071.2018 -6552.7582 33.572969 1.9229778
|
||||
120 262.66442 -5386.2494 -6442.9746 1056.7252 -6587.5499 29.859555 2.7124877
|
||||
130 252.83442 -5422.5444 -6439.7226 1017.1781 -6580.4752 25.979048 1.2031628
|
||||
140 253.85116 -5452.1905 -6473.4591 1021.2686 -6609.489 26.071518 0.30586252
|
||||
150 261.31828 -5490.48 -6541.7895 1051.3096 -6646.6145 16.25855 6.9049978
|
||||
160 255.73681 -5521.6048 -6550.4596 1028.8548 -6658.1518 19.717536 12.339819
|
||||
170 253.42879 -5540.1004 -6559.6697 1019.5694 -6656.688 23.293657 10.289879
|
||||
180 248.51083 -5550.3244 -6550.1084 999.78393 -6661.4181 26.200057 3.433906
|
||||
190 250.80387 -5555.2613 -6564.2703 1009.009 -6666.1497 25.536596 3.3495164
|
||||
SHAKE stats (type/ave/delta) on step 200
|
||||
4 1.111 1.8129e-06
|
||||
6 0.997 7.79639e-07
|
||||
8 1.08 1.08934e-06
|
||||
10 1.111 2.96501e-07
|
||||
12 1.08 4.69175e-07
|
||||
14 0.960001 0
|
||||
18 0.957201 3.76571e-06
|
||||
31 104.52 0.000411069
|
||||
200 251.50575 -5557.4209 -6569.2537 1011.8328 -6674.0864 24.805164 7.1388874
|
||||
colvars: Saving collective variables state to "out.colvars.state".
|
||||
Loop time of 0.653275 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Pair time (%) = 0.47279 (72.3723)
|
||||
Bond time (%) = 0.00182116 (0.278774)
|
||||
Kspace time (%) = 0.079544 (12.1762)
|
||||
Neigh time (%) = 0.0451868 (6.91696)
|
||||
Comm time (%) = 0.027427 (4.19838)
|
||||
Output time (%) = 0.000316501 (0.0484483)
|
||||
Modify time (%) = 0.0247022 (3.78129)
|
||||
Other time (%) = 0.00148731 (0.227671)
|
||||
|
||||
FFT time (% of Kspce) = 0.0109947 (13.8221)
|
||||
FFT Gflps 3d (1d only) = 4.98769 10.1728
|
||||
|
||||
Nlocal: 501 ave 513 max 481 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Nghost: 6556.5 ave 6608 max 6514 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Neighs: 177022 ave 182261 max 172093 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 708086
|
||||
Ave neighs/atom = 353.336
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 7
|
||||
Dangerous builds = 0
|
||||
|
||||
fix 2 all colvars peptide.colvars input out.colvars.state output out2
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.268721
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.01614
|
||||
estimated relative force accuracy = 4.86052e-05
|
||||
using single precision FFTs
|
||||
brick FFT buffer size/proc = 4312 960 3696
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2012-03-23.
|
||||
colvars: # analysis = off [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # colvarsTrajAppend = off [default]
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "out2.colvars.state".
|
||||
colvars: The trajectory file will be "out2.colvars.traj".
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = one
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
|
||||
colvars: All components initialized.
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # lowerWallConstant = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # upperWallConstant = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputSystemForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = two
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
|
||||
colvars: All components initialized.
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # lowerWallConstant = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # upperWallConstant = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputSystemForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 2 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = h_pot
|
||||
colvars: # colvars = { one, two }
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # centers = { 10, 10 }
|
||||
colvars: # targetCenters = { 10, 10 } [default]
|
||||
colvars: # targetForceConstant = 0 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Restarting from file "out.colvars.state".
|
||||
colvars: Restarting collective variable "one" from value: 10.0128
|
||||
colvars: Restarting collective variable "two" from value: 9.62236
|
||||
colvars: Restarting harmonic bias "h_pot".
|
||||
colvars: Reading current stage from the restart.
|
||||
colvars: # stage = 8103505641670189088
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing step number as firstTimestep.
|
||||
SHAKE stats (type/ave/delta) on step 200
|
||||
4 1.111 1.8129e-06
|
||||
6 0.997 7.79639e-07
|
||||
8 1.08 1.08934e-06
|
||||
10 1.111 2.96501e-07
|
||||
12 1.08 4.69175e-07
|
||||
14 0.960001 0
|
||||
18 0.957201 3.76571e-06
|
||||
31 104.52 0.000411069
|
||||
Memory usage per processor = 10.201 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond 2
|
||||
200 251.50575 -5557.4209 -6569.2537 1011.8328 -6674.0864 24.805164 7.1388874
|
||||
210 253.15047 -5538.5669 -6557.0165 1018.4497 -6672.0412 37.671574 0.61297094
|
||||
220 245.19752 -5522.5242 -6508.9784 986.45412 -6628.2001 36.656348 0.048624447
|
||||
230 258.65297 -5495.7177 -6536.3044 1040.5868 -6658.0951 34.855726 0.22046446
|
||||
240 260.8016 -5469.8518 -6519.0827 1049.2309 -6624.173 31.576408 3.757081
|
||||
250 269.06524 -5438.3971 -6520.8735 1082.4764 -6616.3878 25.444134 8.6641098
|
||||
260 266.10241 -5397.317 -6467.8736 1070.5566 -6580.6272 26.87393 8.333095
|
||||
270 272.82004 -5350.8402 -6448.4225 1097.5823 -6563.8152 23.113398 10.972914
|
||||
280 279.52006 -5307.9867 -6432.5238 1124.5371 -6557.7256 33.641067 8.5474809
|
||||
290 286.81221 -5260.8707 -6414.7449 1153.8742 -6515.5413 28.572449 5.9092582
|
||||
SHAKE stats (type/ave/delta) on step 300
|
||||
4 1.111 1.79733e-05
|
||||
6 0.997005 1.02621e-05
|
||||
8 1.08 1.84996e-05
|
||||
10 1.111 9.98591e-06
|
||||
12 1.08 8.83192e-06
|
||||
14 0.960008 0
|
||||
18 0.957203 1.84805e-05
|
||||
31 104.52 0.00169223
|
||||
300 291.51901 -5216.3298 -6389.1399 1172.8101 -6503.1178 27.877408 2.2482392
|
||||
colvars: Saving collective variables state to "out2.colvars.state".
|
||||
Loop time of 0.662081 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Pair time (%) = 0.47307 (71.452)
|
||||
Bond time (%) = 0.00178617 (0.269781)
|
||||
Kspace time (%) = 0.0802494 (12.1208)
|
||||
Neigh time (%) = 0.0528576 (7.98355)
|
||||
Comm time (%) = 0.0277618 (4.19311)
|
||||
Output time (%) = 0.000293612 (0.0443469)
|
||||
Modify time (%) = 0.0245907 (3.71416)
|
||||
Other time (%) = 0.00147164 (0.222275)
|
||||
|
||||
FFT time (% of Kspce) = 0.011487 (14.3141)
|
||||
FFT Gflps 3d (1d only) = 4.77392 9.91625
|
||||
|
||||
Nlocal: 501 ave 514 max 471 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 1 2
|
||||
Nghost: 6609.75 ave 6681 max 6555 min
|
||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||
Neighs: 177036 ave 180240 max 169752 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 1 2
|
||||
|
||||
Total # of neighbors = 708146
|
||||
Ave neighs/atom = 353.366
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 8
|
||||
Dangerous builds = 0
|
||||
|
||||
|
|
@ -0,0 +1,182 @@
|
|||
LAMMPS (21 May 2012-ICMS)
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
3 = max bonds/atom
|
||||
6 = max angles/atom
|
||||
14 = max dihedrals/atom
|
||||
1 = max impropers/atom
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
2004 atoms
|
||||
2004 velocities
|
||||
1365 bonds
|
||||
786 angles
|
||||
207 dihedrals
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
shell "rm -f peptide2.colvars.*"
|
||||
fix 2 all colvars peptide.colvars2 output peptide2
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
|
||||
#dump 1 colvar custom 1 dump.colvar2.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_2
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.268721
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.01614
|
||||
estimated relative force accuracy = 4.86052e-05
|
||||
using single precision FFTs
|
||||
brick FFT buffer size/proc = 10648 3375 5808
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2012-03-23.
|
||||
colvars: # analysis = off [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # colvarsTrajAppend = off [default]
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "peptide2.colvars.state".
|
||||
colvars: The trajectory file will be "peptide2.colvars.traj".
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = one
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: Atom group "group2" defined, 4 initialized: total mass = 15.035.
|
||||
colvars: All components initialized.
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # lowerWallConstant = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # upperWallConstant = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputSystemForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = h_pot
|
||||
colvars: # colvars = { one }
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # centers = { 10 }
|
||||
colvars: # targetCenters = { 10 } [default]
|
||||
colvars: # targetForceConstant = 0 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Memory usage per processor = 22.5865 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond 2
|
||||
0 282.10052 -5237.458 -6372.3765 1134.9186 -6442.7679 16.557152 273.74323
|
||||
10 333.47973 -4982.3893 -6324.0116 1341.6223 -6400.4169 21.367753 12.393269
|
||||
20 309.56974 -4999.4934 -6244.9234 1245.43 -6401.697 43.595449 13.004392
|
||||
30 316.97689 -5025.5598 -6300.7895 1275.2297 -6422.5335 27.323113 6.7588862
|
||||
40 297.5581 -5088.2156 -6285.3215 1197.106 -6395.3714 13.676872 25.625156
|
||||
50 296.80003 -5117.2926 -6311.3488 1194.0562 -6451.8274 30.631279 5.3320296
|
||||
60 281.72797 -5188.4941 -6321.9139 1133.4198 -6427.8834 26.287652 20.573958
|
||||
70 277.26045 -5224.8417 -6340.2882 1115.4465 -6447.8496 27.742888 0.69414894
|
||||
80 268.01458 -5281.8503 -6360.0997 1078.2494 -6496.6064 20.300731 5.2606438
|
||||
90 270.43386 -5334.0846 -6422.067 1087.9824 -6563.2486 39.845993 1.1832496
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11096 0.000191466
|
||||
6 0.996989 3.5552e-05
|
||||
8 1.08 9.1e-06
|
||||
10 1.111 1.58547e-05
|
||||
12 1.08 5.80613e-06
|
||||
14 0.959997 0
|
||||
18 0.957198 2.92453e-05
|
||||
31 104.52 0.00239929
|
||||
100 260.3562 -5387.2263 -6434.6653 1047.439 -6534.1923 20.24674 0.075048834
|
||||
colvars: Saving collective variables state to "peptide2.colvars.state".
|
||||
Loop time of 2.37975 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Pair time (%) = 1.83713 (77.1984)
|
||||
Bond time (%) = 0.00636029 (0.267267)
|
||||
Kspace time (%) = 0.162295 (6.81981)
|
||||
Neigh time (%) = 0.336338 (14.1333)
|
||||
Comm time (%) = 0.0106671 (0.448243)
|
||||
Output time (%) = 0.000264168 (0.0111006)
|
||||
Modify time (%) = 0.024472 (1.02834)
|
||||
Other time (%) = 0.00222516 (0.0935038)
|
||||
|
||||
FFT time (% of Kspce) = 0.028162 (17.3524)
|
||||
FFT Gflps 3d (1d only) = 1.94723 2.85015
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11143 ave 11143 max 11143 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708233 ave 708233 max 708233 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708233
|
||||
Ave neighs/atom = 353.41
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 1
|
||||
|
|
@ -0,0 +1,182 @@
|
|||
LAMMPS (21 May 2012-ICMS)
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
3 = max bonds/atom
|
||||
6 = max angles/atom
|
||||
14 = max dihedrals/atom
|
||||
1 = max impropers/atom
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
2004 atoms
|
||||
2004 velocities
|
||||
1365 bonds
|
||||
786 angles
|
||||
207 dihedrals
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
shell "rm -f peptide2.colvars.*"
|
||||
fix 2 all colvars peptide.colvars2 output peptide2
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
|
||||
#dump 1 colvar custom 1 dump.colvar2.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_2
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.268721
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.01614
|
||||
estimated relative force accuracy = 4.86052e-05
|
||||
using single precision FFTs
|
||||
brick FFT buffer size/proc = 4312 960 3696
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2012-03-23.
|
||||
colvars: # analysis = off [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # colvarsTrajAppend = off [default]
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "peptide2.colvars.state".
|
||||
colvars: The trajectory file will be "peptide2.colvars.traj".
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = one
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: Atom group "group2" defined, 4 initialized: total mass = 15.035.
|
||||
colvars: All components initialized.
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # lowerWallConstant = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # upperWallConstant = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputSystemForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = h_pot
|
||||
colvars: # colvars = { one }
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # centers = { 10 }
|
||||
colvars: # targetCenters = { 10 } [default]
|
||||
colvars: # targetForceConstant = 0 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Memory usage per processor = 10.1924 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond 2
|
||||
0 282.10052 -5237.458 -6372.3765 1134.9186 -6442.7679 16.557152 273.74323
|
||||
10 333.47973 -4982.3893 -6324.0116 1341.6223 -6400.417 21.367753 12.393269
|
||||
20 309.56974 -4999.4934 -6244.9234 1245.43 -6401.697 43.595449 13.004392
|
||||
30 316.97689 -5025.5598 -6300.7896 1275.2297 -6422.5336 27.323113 6.7588863
|
||||
40 297.5581 -5088.2155 -6285.3215 1197.106 -6395.3714 13.676872 25.625156
|
||||
50 296.80003 -5117.2927 -6311.3488 1194.0562 -6451.8275 30.631279 5.3320297
|
||||
60 281.72797 -5188.494 -6321.9138 1133.4198 -6427.8833 26.287652 20.573959
|
||||
70 277.26045 -5224.8417 -6340.2882 1115.4465 -6447.8496 27.742889 0.69414888
|
||||
80 268.01458 -5281.8503 -6360.0997 1078.2494 -6496.6064 20.300731 5.2606437
|
||||
90 270.43386 -5334.0846 -6422.067 1087.9825 -6563.2486 39.845992 1.1832495
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11096 0.000191466
|
||||
6 0.996989 3.5552e-05
|
||||
8 1.08 9.10001e-06
|
||||
10 1.111 1.58547e-05
|
||||
12 1.08 5.80613e-06
|
||||
14 0.959997 0
|
||||
18 0.957198 2.92453e-05
|
||||
31 104.52 0.00239929
|
||||
100 260.35619 -5387.2298 -6434.6688 1047.439 -6534.1958 20.24674 0.07504876
|
||||
colvars: Saving collective variables state to "peptide2.colvars.state".
|
||||
Loop time of 0.650999 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Pair time (%) = 0.466917 (71.7232)
|
||||
Bond time (%) = 0.00176847 (0.271655)
|
||||
Kspace time (%) = 0.0588512 (9.04015)
|
||||
Neigh time (%) = 0.0832494 (12.788)
|
||||
Comm time (%) = 0.0190871 (2.93197)
|
||||
Output time (%) = 0.000295341 (0.0453674)
|
||||
Modify time (%) = 0.0194815 (2.99255)
|
||||
Other time (%) = 0.00134867 (0.20717)
|
||||
|
||||
FFT time (% of Kspce) = 0.010457 (17.7686)
|
||||
FFT Gflps 3d (1d only) = 5.24412 9.93123
|
||||
|
||||
Nlocal: 501 ave 513 max 494 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
Nghost: 6572.5 ave 6593 max 6548 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 177058 ave 181777 max 174301 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 708233
|
||||
Ave neighs/atom = 353.41
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 1
|
||||
|
|
@ -0,0 +1,22 @@
|
|||
configuration {
|
||||
step 200
|
||||
dt 2.000000e+00
|
||||
}
|
||||
|
||||
colvar {
|
||||
name one
|
||||
x 1.00127641579482e+01
|
||||
}
|
||||
|
||||
colvar {
|
||||
name two
|
||||
x 9.62235621950587e+00
|
||||
}
|
||||
|
||||
harmonic {
|
||||
configuration {
|
||||
name h_pot
|
||||
stage 8103505641670189088
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -0,0 +1,102 @@
|
|||
# step one two
|
||||
100 1.00136999784453e+01 1.00648820764882e+01
|
||||
101 1.00137686830422e+01 1.00611307186442e+01
|
||||
102 1.00135851804620e+01 1.00551774768670e+01
|
||||
103 1.00127019172615e+01 1.00448609599088e+01
|
||||
104 1.00107148677220e+01 1.00279880647254e+01
|
||||
105 1.00073753998706e+01 1.00031566249892e+01
|
||||
106 1.00026887490897e+01 9.97035299845099e+00
|
||||
107 9.99696380204809e+00 9.93114513453873e+00
|
||||
108 9.99079173947846e+00 9.88834426761621e+00
|
||||
109 9.98495634348822e+00 9.84525182069547e+00
|
||||
110 9.98029608653331e+00 9.80488128973958e+00
|
||||
111 9.97755063903513e+00 9.76956423088248e+00
|
||||
112 9.97722827031026e+00 9.74089978578719e+00
|
||||
113 9.97952719395978e+00 9.71964890219001e+00
|
||||
114 9.98433213818614e+00 9.70572160189541e+00
|
||||
115 9.99128820986690e+00 9.69882648932897e+00
|
||||
116 9.99993078708906e+00 9.69906675982844e+00
|
||||
117 1.00098268026590e+01 9.70676032193502e+00
|
||||
118 1.00206800068605e+01 9.72193925284532e+00
|
||||
119 1.00323638324515e+01 9.74392975114862e+00
|
||||
120 1.00448758513666e+01 9.77144823009299e+00
|
||||
121 1.00582368252610e+01 9.80293582393448e+00
|
||||
122 1.00723784561855e+01 9.83653845611926e+00
|
||||
123 1.00870571871815e+01 9.86996653086528e+00
|
||||
124 1.01018149909563e+01 9.90067054070927e+00
|
||||
125 1.01159957146856e+01 9.92637090832991e+00
|
||||
126 1.01288197202732e+01 9.94568593115900e+00
|
||||
127 1.01395051017779e+01 9.95858909349258e+00
|
||||
128 1.01474031546764e+01 9.96651060978132e+00
|
||||
129 1.01521102583250e+01 9.97197886676780e+00
|
||||
130 1.01535305336566e+01 9.97782726175993e+00
|
||||
131 1.01518703644018e+01 9.98617108245763e+00
|
||||
132 1.01475651582407e+01 9.99754271679455e+00
|
||||
133 1.01411660808109e+01 1.00106700599276e+01
|
||||
134 1.01332313643590e+01 1.00230219318765e+01
|
||||
135 1.01242577071328e+01 1.00317168123542e+01
|
||||
136 1.01146539200964e+01 1.00343611311947e+01
|
||||
137 1.01047327535065e+01 1.00296410219261e+01
|
||||
138 1.00947009258946e+01 1.00175740354601e+01
|
||||
139 1.00846525340704e+01 9.99930113951843e+00
|
||||
140 1.00745850435896e+01 9.97645596333061e+00
|
||||
141 1.00644392647413e+01 9.95041162930873e+00
|
||||
142 1.00541491709691e+01 9.92180111647481e+00
|
||||
143 1.00436823424749e+01 9.89050169056719e+00
|
||||
144 1.00330636529660e+01 9.85603208426972e+00
|
||||
145 1.00223839228086e+01 9.81818334237853e+00
|
||||
146 1.00118047065649e+01 9.77758921505729e+00
|
||||
147 1.00015612314349e+01 9.73590349870836e+00
|
||||
148 9.99195527218088e+00 9.69551788236989e+00
|
||||
149 9.98332631801527e+00 9.65911749675800e+00
|
||||
150 9.97599491711484e+00 9.62915810268995e+00
|
||||
151 9.97018870425343e+00 9.60717358806770e+00
|
||||
152 9.96597676149386e+00 9.59319263515552e+00
|
||||
153 9.96323912038658e+00 9.58560496094010e+00
|
||||
154 9.96168472712778e+00 9.58154384221214e+00
|
||||
155 9.96091708239459e+00 9.57764409185937e+00
|
||||
156 9.96053284836430e+00 9.57094226701891e+00
|
||||
157 9.96022340231744e+00 9.55966218699141e+00
|
||||
158 9.95984104841431e+00 9.54367921177888e+00
|
||||
159 9.95941115970323e+00 9.52452532866834e+00
|
||||
160 9.95909775592352e+00 9.50490062318069e+00
|
||||
161 9.95913472197875e+00 9.48781177595095e+00
|
||||
162 9.95973716567135e+00 9.47562216260840e+00
|
||||
163 9.96102283681378e+00 9.46939618474568e+00
|
||||
164 9.96297512061468e+00 9.46883909503368e+00
|
||||
165 9.96545450087319e+00 9.47284744786104e+00
|
||||
166 9.96824446676367e+00 9.48032505757766e+00
|
||||
167 9.97111490093449e+00 9.49080999053287e+00
|
||||
168 9.97388723087919e+00 9.50468382474366e+00
|
||||
169 9.97648454853684e+00 9.52297944488190e+00
|
||||
170 9.97895120221314e+00 9.54683939172159e+00
|
||||
171 9.98143439573287e+00 9.57673744631037e+00
|
||||
172 9.98412851702981e+00 9.61177677879831e+00
|
||||
173 9.98719912546727e+00 9.64941646139346e+00
|
||||
174 9.99071466036109e+00 9.68581516318204e+00
|
||||
175 9.99461255041478e+00 9.71674194992540e+00
|
||||
176 9.99871362276481e+00 9.73875618365856e+00
|
||||
177 1.00027752607551e+01 9.75023319932384e+00
|
||||
178 1.00065593228689e+01 9.75187374895997e+00
|
||||
179 1.00098932819698e+01 9.74651102922357e+00
|
||||
180 1.00127089751067e+01 9.73824323715410e+00
|
||||
181 1.00150539578018e+01 9.73118937807432e+00
|
||||
182 1.00170703552922e+01 9.72834303011533e+00
|
||||
183 1.00189424568686e+01 9.73087964994846e+00
|
||||
184 1.00208211796404e+01 9.73798531353725e+00
|
||||
185 1.00227525196798e+01 9.74722518450810e+00
|
||||
186 1.00246411639883e+01 9.75544038568881e+00
|
||||
187 1.00262714680409e+01 9.75985920611179e+00
|
||||
188 1.00273770464779e+01 9.75895332491778e+00
|
||||
189 1.00277296204562e+01 9.75275348211835e+00
|
||||
190 1.00272109105395e+01 9.74260945002776e+00
|
||||
191 1.00258469602549e+01 9.73056029017316e+00
|
||||
192 1.00238019119674e+01 9.71852969006276e+00
|
||||
193 1.00213411099718e+01 9.70760780505631e+00
|
||||
194 1.00187745961566e+01 9.69771723529251e+00
|
||||
195 1.00163957858114e+01 9.68783387106584e+00
|
||||
196 1.00144342355802e+01 9.67665900893200e+00
|
||||
197 1.00130379562453e+01 9.66342567131686e+00
|
||||
198 1.00122840592666e+01 9.64853643967174e+00
|
||||
199 1.00121986038636e+01 9.63383126934824e+00
|
||||
200 1.00127641579482e+01 9.62235621950587e+00
|
||||
|
|
@ -0,0 +1,22 @@
|
|||
configuration {
|
||||
step 300
|
||||
dt 2.000000e+00
|
||||
}
|
||||
|
||||
colvar {
|
||||
name one
|
||||
x 9.95354148699614e+00
|
||||
}
|
||||
|
||||
colvar {
|
||||
name two
|
||||
x 9.79310294857288e+00
|
||||
}
|
||||
|
||||
harmonic {
|
||||
configuration {
|
||||
name h_pot
|
||||
stage 8103505641670189088
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -0,0 +1,102 @@
|
|||
# step one two
|
||||
200 1.00127641579482e+01 9.62235621950587e+00
|
||||
201 1.00139098397954e+01 9.61766067322651e+00
|
||||
202 1.00154895322849e+01 9.62284260846102e+00
|
||||
203 1.00172625720562e+01 9.63964717046032e+00
|
||||
204 1.00188930177704e+01 9.66786064733448e+00
|
||||
205 1.00199761813056e+01 9.70519780219794e+00
|
||||
206 1.00200944106384e+01 9.74779969655747e+00
|
||||
207 1.00188963572281e+01 9.79111374012340e+00
|
||||
208 1.00161883604793e+01 9.83086787098858e+00
|
||||
209 1.00120201470551e+01 9.86403984083060e+00
|
||||
210 1.00067290723642e+01 9.88948240692241e+00
|
||||
211 1.00009114042457e+01 9.90790280320401e+00
|
||||
212 9.99530858712775e+00 9.92119319076851e+00
|
||||
213 9.99063126799011e+00 9.93149262690681e+00
|
||||
214 9.98737350983788e+00 9.94043951053174e+00
|
||||
215 9.98567811211086e+00 9.94878566374960e+00
|
||||
216 9.98529977833156e+00 9.95640488686023e+00
|
||||
217 9.98567740511041e+00 9.96270367197379e+00
|
||||
218 9.98609281741416e+00 9.96726160094494e+00
|
||||
219 9.98586784093273e+00 9.97033437532426e+00
|
||||
220 9.98454831898211e+00 9.97291246609646e+00
|
||||
221 9.98202887687821e+00 9.97627400695988e+00
|
||||
222 9.97858776161328e+00 9.98128372296812e+00
|
||||
223 9.97481791063232e+00 9.98787692577356e+00
|
||||
224 9.97146915301902e+00 9.99495319867179e+00
|
||||
225 9.96924741695340e+00 1.00005781312739e+01
|
||||
226 9.96863280571612e+00 1.00023562928510e+01
|
||||
227 9.96977462939505e+00 9.99793468396390e+00
|
||||
228 9.97249206995624e+00 9.98558877312050e+00
|
||||
229 9.97637419760570e+00 9.96476526430303e+00
|
||||
230 9.98093600414111e+00 9.93639297716863e+00
|
||||
231 9.98577334632368e+00 9.90279138444459e+00
|
||||
232 9.99066901099700e+00 9.86714667869485e+00
|
||||
233 9.99562704815141e+00 9.83274230148512e+00
|
||||
234 1.00008356809073e+01 9.80226834521352e+00
|
||||
235 1.00065772362800e+01 9.77744581513232e+00
|
||||
236 1.00131097048912e+01 9.75894408214992e+00
|
||||
237 1.00205553485494e+01 9.74639403983496e+00
|
||||
238 1.00288314258010e+01 9.73851464709533e+00
|
||||
239 1.00376482262668e+01 9.73355843502651e+00
|
||||
240 1.00465718867162e+01 9.72986544373201e+00
|
||||
241 1.00551241447104e+01 9.72616365347388e+00
|
||||
242 1.00628799016098e+01 9.72156081057173e+00
|
||||
243 1.00695359569141e+01 9.71533506969961e+00
|
||||
244 1.00749394351078e+01 9.70669135454371e+00
|
||||
245 1.00790729024702e+01 9.69470862769774e+00
|
||||
246 1.00820010382698e+01 9.67869454326621e+00
|
||||
247 1.00837917095021e+01 9.65894101136318e+00
|
||||
248 1.00844414119874e+01 9.63696223650643e+00
|
||||
249 1.00838441989246e+01 9.61423476365400e+00
|
||||
250 1.00818306797879e+01 9.59185059543549e+00
|
||||
251 1.00782686429397e+01 9.57154356576350e+00
|
||||
252 1.00731806695096e+01 9.55550278600070e+00
|
||||
253 1.00668200834919e+01 9.54554307033366e+00
|
||||
254 1.00596730176507e+01 9.54248962932697e+00
|
||||
255 1.00523895763009e+01 9.54590976255577e+00
|
||||
256 1.00456784264533e+01 9.55421544253452e+00
|
||||
257 1.00402005024002e+01 9.56513899116782e+00
|
||||
258 1.00364831006552e+01 9.57640458000444e+00
|
||||
259 1.00348576492106e+01 9.58619146455749e+00
|
||||
260 1.00354210621162e+01 9.59329709957898e+00
|
||||
261 1.00380245202744e+01 9.59728096353517e+00
|
||||
262 1.00422960600822e+01 9.59832037848005e+00
|
||||
263 1.00476990763950e+01 9.59672497993560e+00
|
||||
264 1.00536104533027e+01 9.59261911381189e+00
|
||||
265 1.00594002482137e+01 9.58602304006163e+00
|
||||
266 1.00644981793165e+01 9.57714719542419e+00
|
||||
267 1.00684482704210e+01 9.56662135439055e+00
|
||||
268 1.00709580655557e+01 9.55551489305294e+00
|
||||
269 1.00719418900228e+01 9.54518226195314e+00
|
||||
270 1.00715463773733e+01 9.53703197862875e+00
|
||||
271 1.00701345227997e+01 9.53228911010047e+00
|
||||
272 1.00682184887617e+01 9.53176321322706e+00
|
||||
273 1.00663378629920e+01 9.53558933249131e+00
|
||||
274 1.00649132448630e+01 9.54304329234477e+00
|
||||
275 1.00641243212406e+01 9.55266696753925e+00
|
||||
276 1.00638595454980e+01 9.56275901409309e+00
|
||||
277 1.00637587244679e+01 9.57196213233751e+00
|
||||
278 1.00633313189549e+01 9.57961568108488e+00
|
||||
279 1.00621123193119e+01 9.58575692732997e+00
|
||||
280 1.00598117112007e+01 9.59088855190189e+00
|
||||
281 1.00564177173993e+01 9.59570566223894e+00
|
||||
282 1.00522270044392e+01 9.60088836897012e+00
|
||||
283 1.00477888199161e+01 9.60693590561625e+00
|
||||
284 1.00437690523107e+01 9.61400570555926e+00
|
||||
285 1.00407622307256e+01 9.62182265962647e+00
|
||||
286 1.00391028258991e+01 9.62979902243492e+00
|
||||
287 1.00387366035163e+01 9.63738040674711e+00
|
||||
288 1.00391979793082e+01 9.64439605217689e+00
|
||||
289 1.00397008587343e+01 9.65118231683256e+00
|
||||
290 1.00393154139857e+01 9.65847479887268e+00
|
||||
291 1.00371856971467e+01 9.66716430247627e+00
|
||||
292 1.00327325013742e+01 9.67799413246555e+00
|
||||
293 1.00257889436952e+01 9.69130066948859e+00
|
||||
294 1.00166284740574e+01 9.70687426338097e+00
|
||||
295 1.00058767991341e+01 9.72395332252100e+00
|
||||
296 9.99433972822595e+00 9.74134088397850e+00
|
||||
297 9.98281255441855e+00 9.75768650006539e+00
|
||||
298 9.97193339524040e+00 9.77194269576588e+00
|
||||
299 9.96211387496966e+00 9.78370254738211e+00
|
||||
300 9.95354148699614e+00 9.79310294857288e+00
|
||||
|
|
@ -0,0 +1,39 @@
|
|||
# collective variable example: monitor distances
|
||||
|
||||
colvarsTrajFrequency 1 # output every 10 steps
|
||||
colvarsRestartFrequency 1000
|
||||
|
||||
colvar {
|
||||
name one
|
||||
|
||||
distance {
|
||||
group1 {
|
||||
atomNumbers 2 4 5 6
|
||||
}
|
||||
group2 {
|
||||
atomNumbers 37
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
colvar {
|
||||
name two
|
||||
|
||||
distance {
|
||||
group1 {
|
||||
atomNumbers 80 82 83 84
|
||||
}
|
||||
group2 {
|
||||
atomNumbers 37
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
harmonic {
|
||||
name h_pot
|
||||
colvars one two
|
||||
centers 10.00 10.0
|
||||
forceConstant 100.0 100.0
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -0,0 +1,26 @@
|
|||
# collective variable example: monitor distances
|
||||
|
||||
colvarsTrajFrequency 1 # output every 10 steps
|
||||
colvarsRestartFrequency 1000
|
||||
|
||||
colvar {
|
||||
name one
|
||||
|
||||
distance {
|
||||
group1 {
|
||||
atomNumbers 2 4 5 6
|
||||
}
|
||||
group2 {
|
||||
atomNumbers 80 82 83 84
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
harmonic {
|
||||
name h_pot
|
||||
colvars one
|
||||
centers 10.00
|
||||
forceConstant 100.0
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -0,0 +1,126 @@
|
|||
PSF
|
||||
|
||||
1 !NTITLE
|
||||
REMARKS VMD-generated NAMD/X-Plor PSF structure file
|
||||
|
||||
84 !NATOM
|
||||
1 0 UNK O O 0.000000 12.0000 0
|
||||
2 0 UNK C C 0.000000 12.0000 0
|
||||
3 0 UNK O O 0.000000 12.0000 0
|
||||
4 0 UNK H H 0.000000 12.0000 0
|
||||
5 0 UNK H H 0.000000 12.0000 0
|
||||
6 0 UNK H H 0.000000 12.0000 0
|
||||
7 0 UNK C C 0.000000 12.0000 0
|
||||
8 0 UNK C C 0.000000 12.0000 0
|
||||
9 0 UNK O O 0.000000 12.0000 0
|
||||
10 0 UNK O O 0.000000 12.0000 0
|
||||
11 0 UNK C C 0.000000 12.0000 0
|
||||
12 0 UNK C C 0.000000 12.0000 0
|
||||
13 0 UNK C C 0.000000 12.0000 0
|
||||
14 0 UNK C C 0.000000 12.0000 0
|
||||
15 0 UNK C C 0.000000 12.0000 0
|
||||
16 0 UNK C C 0.000000 12.0000 0
|
||||
17 0 UNK C C 0.000000 12.0000 0
|
||||
18 0 UNK O O 0.000000 12.0000 0
|
||||
19 0 UNK 10 10 0.000000 12.0000 0
|
||||
20 0 UNK H H 0.000000 12.0000 0
|
||||
21 0 UNK H H 0.000000 12.0000 0
|
||||
22 0 UNK H H 0.000000 12.0000 0
|
||||
23 0 UNK 11 11 0.000000 12.0000 0
|
||||
24 0 UNK 11 11 0.000000 12.0000 0
|
||||
25 0 UNK 11 11 0.000000 12.0000 0
|
||||
26 0 UNK 11 11 0.000000 12.0000 0
|
||||
27 0 UNK 10 10 0.000000 12.0000 0
|
||||
28 0 UNK C C 0.000000 12.0000 0
|
||||
29 0 UNK C C 0.000000 12.0000 0
|
||||
30 0 UNK O O 0.000000 12.0000 0
|
||||
31 0 UNK O O 0.000000 12.0000 0
|
||||
32 0 UNK 10 10 0.000000 12.0000 0
|
||||
33 0 UNK H H 0.000000 12.0000 0
|
||||
34 0 UNK H H 0.000000 12.0000 0
|
||||
35 0 UNK C C 0.000000 12.0000 0
|
||||
36 0 UNK C C 0.000000 12.0000 0
|
||||
37 0 UNK O O 0.000000 12.0000 0
|
||||
38 0 UNK O O 0.000000 12.0000 0
|
||||
39 0 UNK 10 10 0.000000 12.0000 0
|
||||
40 0 UNK H H 0.000000 12.0000 0
|
||||
41 0 UNK H H 0.000000 12.0000 0
|
||||
42 0 UNK C C 0.000000 12.0000 0
|
||||
43 0 UNK C C 0.000000 12.0000 0
|
||||
44 0 UNK O O 0.000000 12.0000 0
|
||||
45 0 UNK O O 0.000000 12.0000 0
|
||||
46 0 UNK C C 0.000000 12.0000 0
|
||||
47 0 UNK C C 0.000000 12.0000 0
|
||||
48 0 UNK C C 0.000000 12.0000 0
|
||||
49 0 UNK C C 0.000000 12.0000 0
|
||||
50 0 UNK C C 0.000000 12.0000 0
|
||||
51 0 UNK C C 0.000000 12.0000 0
|
||||
52 0 UNK C C 0.000000 12.0000 0
|
||||
53 0 UNK 10 10 0.000000 12.0000 0
|
||||
54 0 UNK H H 0.000000 12.0000 0
|
||||
55 0 UNK H H 0.000000 12.0000 0
|
||||
56 0 UNK H H 0.000000 12.0000 0
|
||||
57 0 UNK 11 11 0.000000 12.0000 0
|
||||
58 0 UNK 11 11 0.000000 12.0000 0
|
||||
59 0 UNK 11 11 0.000000 12.0000 0
|
||||
60 0 UNK 11 11 0.000000 12.0000 0
|
||||
61 0 UNK 11 11 0.000000 12.0000 0
|
||||
62 0 UNK C C 0.000000 12.0000 0
|
||||
63 0 UNK C C 0.000000 12.0000 0
|
||||
64 0 UNK O O 0.000000 12.0000 0
|
||||
65 0 UNK O O 0.000000 12.0000 0
|
||||
66 0 UNK C C 0.000000 12.0000 0
|
||||
67 0 UNK C C 0.000000 12.0000 0
|
||||
68 0 UNK 12 12 0.000000 12.0000 0
|
||||
69 0 UNK C C 0.000000 12.0000 0
|
||||
70 0 UNK 10 10 0.000000 12.0000 0
|
||||
71 0 UNK H H 0.000000 12.0000 0
|
||||
72 0 UNK H H 0.000000 12.0000 0
|
||||
73 0 UNK H H 0.000000 12.0000 0
|
||||
74 0 UNK H H 0.000000 12.0000 0
|
||||
75 0 UNK H H 0.000000 12.0000 0
|
||||
76 0 UNK H H 0.000000 12.0000 0
|
||||
77 0 UNK H H 0.000000 12.0000 0
|
||||
78 0 UNK H H 0.000000 12.0000 0
|
||||
79 0 UNK C C 0.000000 12.0000 0
|
||||
80 0 UNK C C 0.000000 12.0000 0
|
||||
81 0 UNK 10 10 0.000000 12.0000 0
|
||||
82 0 UNK H H 0.000000 12.0000 0
|
||||
83 0 UNK H H 0.000000 12.0000 0
|
||||
84 0 UNK H H 0.000000 12.0000 0
|
||||
|
||||
0 !NBOND: bonds
|
||||
|
||||
|
||||
0 !NTHETA: angles
|
||||
|
||||
|
||||
0 !NPHI: dihedrals
|
||||
|
||||
|
||||
0 !NIMPHI: impropers
|
||||
|
||||
|
||||
0 !NDON: donors
|
||||
|
||||
|
||||
0 !NACC: acceptors
|
||||
|
||||
|
||||
0 !NNB
|
||||
|
||||
0 0 0 0 0 0 0 0
|
||||
0 0 0 0 0 0 0 0
|
||||
0 0 0 0 0 0 0 0
|
||||
0 0 0 0 0 0 0 0
|
||||
0 0 0 0 0 0 0 0
|
||||
0 0 0 0 0 0 0 0
|
||||
0 0 0 0 0 0 0 0
|
||||
0 0 0 0 0 0 0 0
|
||||
0 0 0 0 0 0 0 0
|
||||
0 0 0 0 0 0 0 0
|
||||
0 0 0 0
|
||||
|
||||
1 0 !NGRP
|
||||
0 0 0
|
||||
|
||||
|
|
@ -0,0 +1,17 @@
|
|||
configuration {
|
||||
step 100
|
||||
dt 2.000000e+00
|
||||
}
|
||||
|
||||
colvar {
|
||||
name one
|
||||
x 1.00387424212228e+01
|
||||
}
|
||||
|
||||
harmonic {
|
||||
configuration {
|
||||
name h_pot
|
||||
stage 4044288781530052640
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -0,0 +1,102 @@
|
|||
# step one
|
||||
0 1.23398428397332e+01
|
||||
1 1.23379000531837e+01
|
||||
2 1.22833752132682e+01
|
||||
3 1.21783464524822e+01
|
||||
4 1.20268109152646e+01
|
||||
5 1.18342676552027e+01
|
||||
6 1.16071240696111e+01
|
||||
7 1.13522568477758e+01
|
||||
8 1.10769760454451e+01
|
||||
9 1.07892333501017e+01
|
||||
10 1.04978607983300e+01
|
||||
11 1.02148368912480e+01
|
||||
12 9.95820967758655e+00
|
||||
13 9.74528082635713e+00
|
||||
14 9.59065550809125e+00
|
||||
15 9.49025917553263e+00
|
||||
16 9.43254360388750e+00
|
||||
17 9.41011962734900e+00
|
||||
18 9.41602364253240e+00
|
||||
19 9.44413444723206e+00
|
||||
20 9.49001191595699e+00
|
||||
21 9.55036186844267e+00
|
||||
22 9.62258413071055e+00
|
||||
23 9.70460340526413e+00
|
||||
24 9.79475248209609e+00
|
||||
25 9.89135077720185e+00
|
||||
26 9.99213105078110e+00
|
||||
27 1.00938499722663e+01
|
||||
28 1.01925349210626e+01
|
||||
29 1.02845107805173e+01
|
||||
30 1.03676652352347e+01
|
||||
31 1.04416367894860e+01
|
||||
32 1.05071334937552e+01
|
||||
33 1.05650452299048e+01
|
||||
34 1.06158824214188e+01
|
||||
35 1.06595186275218e+01
|
||||
36 1.06948928511102e+01
|
||||
37 1.07202580715959e+01
|
||||
38 1.07337399401028e+01
|
||||
39 1.07331885445159e+01
|
||||
40 1.07158932314825e+01
|
||||
41 1.06789136129953e+01
|
||||
42 1.06198862520319e+01
|
||||
43 1.05380120055201e+01
|
||||
44 1.04346603936480e+01
|
||||
45 1.03132931131809e+01
|
||||
46 1.01792839195940e+01
|
||||
47 1.00398967921774e+01
|
||||
48 9.90373826474332e+00
|
||||
49 9.77934819842326e+00
|
||||
50 9.67344128626180e+00
|
||||
51 9.58957431460176e+00
|
||||
52 9.52771755964755e+00
|
||||
53 9.48463676001684e+00
|
||||
54 9.45495927636316e+00
|
||||
55 9.43277262066999e+00
|
||||
56 9.41329687195946e+00
|
||||
57 9.39418023785890e+00
|
||||
58 9.37608079167942e+00
|
||||
59 9.36244026161597e+00
|
||||
60 9.35853356967195e+00
|
||||
61 9.36993825765332e+00
|
||||
62 9.40084295384763e+00
|
||||
63 9.45286334548428e+00
|
||||
64 9.52464492798022e+00
|
||||
65 9.61230778865749e+00
|
||||
66 9.71074173620872e+00
|
||||
67 9.81506921139973e+00
|
||||
68 9.92117599348263e+00
|
||||
69 1.00244217575122e+01
|
||||
70 1.01178260477346e+01
|
||||
71 1.01986938379172e+01
|
||||
72 1.02670956368544e+01
|
||||
73 1.03213051063305e+01
|
||||
74 1.03597191337854e+01
|
||||
75 1.03817745676591e+01
|
||||
76 1.03880610583944e+01
|
||||
77 1.03809103738027e+01
|
||||
78 1.03645558156884e+01
|
||||
79 1.03441497701913e+01
|
||||
80 1.03243653409000e+01
|
||||
81 1.03082112818858e+01
|
||||
82 1.02961296917318e+01
|
||||
83 1.02862106580352e+01
|
||||
84 1.02756069146933e+01
|
||||
85 1.02618115908758e+01
|
||||
86 1.02435132305408e+01
|
||||
87 1.02212121470422e+01
|
||||
88 1.01972799936680e+01
|
||||
89 1.01743931780361e+01
|
||||
90 1.01538342930689e+01
|
||||
91 1.01363020288600e+01
|
||||
92 1.01223080393853e+01
|
||||
93 1.01118050646187e+01
|
||||
94 1.01038513159042e+01
|
||||
95 1.00967020139234e+01
|
||||
96 1.00885782989097e+01
|
||||
97 1.00784257293241e+01
|
||||
98 1.00661428832570e+01
|
||||
99 1.00524912515310e+01
|
||||
100 1.00387424212228e+01
|
||||
Loading…
Reference in New Issue