[gmx-users] Changing mdp options for a restart
dgfd dgdfg
roinato at mail.ru
Sat Jan 12 16:47:05 CET 2019
http://manual.gromacs.org/documentation/current/user-guide/managing-simulations.html#changing-mdp-options-for-a-restart
I tried to simulate instantaneous perturbation in topology and did everything as in instruction (below).
Changing mdp options for a restart
If you wish to make changes to your simulations settings other than length, then you should do so in the mdp file or topology, and then call
gmx grompp -f possibly-changed.mdp -p possibly-changed.top -c state.cpt -o new.tpr
gmx mdrun -s new.tpr -cpi state.cpt
to instruct gmx grompp to copy the full-precision coordinates in the checkpoint file into the new tpr file. You should consider your choices for tinit , init-step , nsteps and simulation-part . You should generally not regenerate velocities with gen-vel , and generally select continuation so that constraints are not re-applied before the first integration step. My steps are:
gmx grompp -f -p -c 4-daspi-S0.gro -o S0 ; old topology compilation
gmx mdrun -v -deffnm S0 ; old run
gmx grompp -f grompp-S1.mdp -p topol-S1.top -c S0.cpt -o S1 ; here begins actual part
But I got error message from "gmx grompp, version 2019"
Error in user input:
Invalid command-line options
In command-line option -c
File name 'S0.cpt' cannot be used for this option.
Only the following extensions are possible:
.gro, .g96, .pdb, .brk, .ent, .esp, .tpr
What is the reason of mistake, or something wrong in manual?
More information about the gromacs.org_gmx-users
mailing list