[gmx-users] Energy Minimization
saipooja at gmail.com
Mon Oct 18 22:26:16 CEST 2010
I am using CHARMM forcefield with tables for Protein SOL interactions for
Tables supplied: table.xvg, table_Protein_SOL.xvg, tablep.xvg (Standard
tables for 6-12 interactions used)
Combination rule changed from '2' to '1' in forcefield.itp file.
In the energy minimization step, using mdrun the following problem is
Polak-Ribiere Conjugate Gradients:
Tolerance (Fmax) = 1.00000e+00
Number of steps = 10000
F-max = 2.98523e+10 on atom 4
F-Norm = 1.32072e+09
step -1: Water molecule starting at atom 1149 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
title = Energy Minimization ; Title of run
; The following line tell the program the standard locations where to find
cpp = /lib/cpp ; Preprocessor
; Define can be used to control processes
;define = -DFLEXIBLE
define = -DPOSRES
; Parameters describing what to do, when to stop and what to save
integrator = cg ; Algorithm (steep = steepest descent
emtol = 1.0 ; Stop minimization when the maximum force <
nsteps = 10000 ; Maximum number of (minimization) steps to
nstenergy = 10000 ; Write energies to disk every nstenergy
energygrps = Protein SOL
energygrp_table = Protein SOL
; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
ns_type = grid ; Method to determine neighbor list (simple,
coulombtype = User ; Treatment of long range electrostatic interactions
rcoulomb = 1.0 ; long range electrostatic cut-off
rvdw = 1.0 ; long range Van der Waals cut-off
constraints = none ; Bond types to replace by constraints
pbc = xyz ; Periodic Boundary Conditions (yes/no)
Quaerendo Invenietis-Seek and you shall discover.
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