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#!/bin/csh
Generated by CHARMM-GUI (http://www.charmm-gui.org)
This folder contains GROMACS formatted CHARMM36 force fields, a pre-optimized PDB structure, and GROMACS inputs.
All input files were optimized for GROMACS 2019.2 or above, so lower version of GROMACS can cause some errors.
We adopted the Verlet cut-off scheme for all minimization, equilibration, and production steps because it is
faster and more accurate than the group scheme. If you have a trouble with a performance of Verlet scheme while
running parallelized simulation, you should check if you are using appropriate command line.
For MPI parallelizing, we recommand following command:
mpirun -np $NUM_CPU gmx mdrun -ntomp 1
Minimization
In the case that there is a problem during minimization using a single precision of GROMACS, please try to use
a double precision of GROMACS only for the minimization step.
step6.0
gmx grompp -f step6.0_minimization.mdp -o step6.0_minimization.tpr -c step5_input.gro -r step5_input.gro -p topol.top
gmx_d mdrun -v -deffnm step6.0_minimization
Equilibration
set cnt = 1
set cntmax = 6
while ( {cnt} <= {cntmax} )
@ pcnt = {cnt} - 1
if ( {cnt} == 1 ) then
gmx grompp -f step6.{$cnt}_equilibration.mdp -o step6.{$cnt}_equilibration.tpr -c step6.{$pcnt}_minimization.gro -r step5_input.gro -p topol.top
gmx mdrun -v -deffnm step6.{$cnt}_equilibration
else
gmx grompp -f step6.{$cnt}_equilibration.mdp -o step6.{$cnt}_equilibration.tpr -c step6.{$pcnt}_equilibration.gro -r step5_input.gro -p topol.top
gmx mdrun -v -deffnm step6.{$cnt}_equilibration
endif
@ cnt += 1
end
Production
set cnt = 1
set cntmax = 10
while ( {cnt} <= {cntmax} )
if ( {cnt} == 1 ) then
gmx grompp -f step7_production.mdp -o step7_{cnt}.tpr -c step6.6_equilibration.gro -p topol.top
gmx mdrun -v -deffnm step7_{cnt}
else
@ pcnt = {cnt} - 1
gmx grompp -f step7_production.mdp -o step7_{cnt}.tpr -c step7_{pcnt}.gro -t step7_{pcnt}.cpt -p topol.top
gmx mdrun -v -deffnm step7_{cnt}
endif
@ cnt += 1
end
The run stopped at 6.1 step, stuck at 6.2 step how to continue from 6.2 step or restart from any step