Production run mdp file

User discussions
1

GROMACS version:
GROMACS modification: Yes/No

Is it necessary to keep continuation = yes in the mdp file during the production run?

I have run my simulation with the following command and the results so far seem fine.
gmx_mpi grompp -f prod.mdp -c NPT.gro -r NPT.gro -t NPT.cpt -p *.top -n *.ndx -o prod.tpr

Can gromacs not start the simulation from the NPT checkpoint file?

2

If you want to continue under identical conditions, you don’t need grompp, but typically when people refer to NPT vs. production, it’s because it’s the end of an equilibration period under the influence of restraints. In that case, you’re changing the input settings by removing restraints, therefore you do need to use grompp and appropriately account for constraint lengths that were already solved via the continuation keyword.

3

Thank you for your reply.

I am running a NVT production run under the effect of restraints. So is it okay to not give the continuation option?

4

If you are constraining bonds and are continuing on from a previous simulation that used constraints (not restraints, that’s totally different), then you need the continuation keyword set appropriately.

5

I am not using any constraints on the bonds. Thank you for clearing my doubt.

6

Hello, I have a similar question to this one and I wanted to resolve some of my confusion about it if possible.

If I want to continue a simulation correctly (with the previous positions/velocities/internal variables loaded) and I want to change the temperature and/or pressure from one step to the next, is it sufficient to just load the checkpoint file into grompp or must I also load the checkpoint file into mdrun again? I am just not sure what the grompp -t step accomplishes versus the mdrun -cpi step because it seems to me as though the information in the checkpoint only has to be loaded once. I want to make sure that my simulation is restarting in the “right” way because these simulations are quite costly and > 6 microseconds.

Example:
gmx grompp -f step2.mdp -t step1.cpt -o step2.tpr -c system.gro -p topol.top
gmx mdrun -v -deffnm step2

OR

gmx grompp -f step2.mdp -t step1.cpt -o step2.tpr -c system.gro -p topol.top
gmx mdrun -v -cpi step1.cpt -deffnm step2

^What is the difference between the two cases listed above?

Thank you for any insight on this!

7

I had the same question and the most information I could find is:

If you wish to change the ensemble or things like output frequency, then supplying the checkpoint file to gmx grompp with -t along with a new .mdp file with -f is the recommended procedure. Actually preserving the ensemble (if possible) still requires passing the checkpoint file to gmx mdrun -cpi .

from gmx-grompp(1) — gromacs-data — Debian experimental — Debian Manpages.

So I believe to preserve as much information as possible, you should include the checkpoint file in both gmx grompp and mdrun commands.