CSh loop script-Restart the following equilibration run due to termination caused by shutdown

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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


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.


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


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
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
@ cnt += 1


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}
@ cnt += 1

The run stopped at 6.1 step, stuck at 6.2 step how to continue from 6.2 step or restart from any step

What was the output given at “step 6.1”? What was written to the terminal? What was written to the log files?