Error in changing mdp options for a restart

User discussions
1

GROMACS version: 2020.2
GROMACS modification: No
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Hi,

I’m trying to restart my simulation using a check point file with modified mdp options, and when I run the following command (command from the User guide):

gmx_mpi grompp -f md.mdp -p topol.top -c md_0_60.cpt -o md_0_60.tpr

I get the following error:

Error in user input:
Invalid command-line options
In command-line option -c
File name ‘md_0_60.cpt’ cannot be used for this option.
Only the following extensions are possible:
.gro, .g96, .pdb, .brk, .ent, .esp, .tpr

In the command template, .cpt file is required for the option -c, so I’m not sure why I’m getting this error. All the files (md.mdp, topol.top and md_0_60.cpt) are in the working directory.
Thank you for your help in advance.

2

Hi,
As the error message says, cpt extension can not be used as input for grompp (see
gmx grompp — GROMACS 2021 documentation).

It depends which options you want to change in the mdp. You can generate a tpr in the following way

  1. if you want just to extend the simulation you can use gmx convert-tpr — GROMACS 2021 documentation
  2. if you want to change more option, you can use gmx grompp and -c last frame (of previous simulation) as input. If you want you use both positions and velocities of the last frame, put gen_vel= no as option in mdp file
    Best regards
    Alessandra
3

Hi Alessandra,

Thank you for your reply.
For the restart, I want to run the simulation with the smaller time step (originally 2fs, but I want to change it to 1fs), so I followed what the GROMACS 2020.2 User guide (Managing long simulations — GROMACS 2020.2 documentation) said as follows:

“”"""
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.
“”"""

However, cpt extension cannot be used with the option -c:

  1. You suggested to use “-c last frame” instead. Does this mean to get the last frame as .gro or .pdb file?
  2. I saw in the User guide you shared me that -t extension actually takes .cpt file. Since the error I got only said " In command-line option -c. File name ‘md_0_60.cpt’ cannot be used for this option.", would it be possible to use option -t and use .cpt file?

Thank you for your help.

4

Hi,
Yes, sure both option works.
Alessandra

5

Great, thank you.