[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?


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