Solution Builder in www.charmm-gui.org

User discussions
1

GROMACS version:
GROMACS modification:
What is the purpose of these repetitions and if I want to continue the simulation, which step should I choose?

Production

set cnt = 1
set cntmax = 10

while ( {cnt} <= {cntmax} )
@ pcnt = {cnt} - 1 set istep = {prod_step}{cnt} set pstep = {prod_step}${pcnt}

if ( ${cnt} == 1 ) then
    set pstep = ${equi_prefix}
    gmx grompp -f ${prod_prefix}.mdp -o ${istep}.tpr -c ${pstep}.gro -p topol.top -n index.ndx
else
    gmx grompp -f ${prod_prefix}.mdp -o ${istep}.tpr -c ${pstep}.gro -t ${pstep}.cpt -p topol.top -n index.ndx
endif
gmx mdrun -v -deffnm ${istep}
@ cnt += 1

end

2

If you have your equilibration part performed correctly, you can just as well do the production in a single step (with automatic gromacs restarts), there’s no point in regenerating the .tpr after each iteration, besides perhaps having backups if anything gets corrupted and you need to restart from an earlier timestamp.

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