Managing long simulations (restart and new MD2 run cases)?

User discussions
1

GROMACS version: :-) GROMACS - gmx mdrun, 2020.5 (double precision) (-:

Hello Everyone,
I have a query regarding the restart of running a second simulation with extension of time.

I have used the commands (for example),
gmx convert-tpr -s MD1.tpr -extend 10 -o MD2.tpr
gmx mdrun -s MD2.tpr -cpi MD1.cpt

MD1 → 10 ps, MD2 → 10 ps (extension)
But I found MD2.tpr calculates from 0 ps to 20 ps.

The bash script is copy the MD2.tpr and MD1.cpt to the compute node. I am guessing, as MD1.xtc/.log/.trr/.gro files are not copied, so MD2 starts from begining 0ps and ends at 20 ps to complete the full run.

Am I correct here? Do we need to copy all files MD1.gro, MD1.xtc, MD1.log, MD1.trr, MD1.cpt?

Can anyone suggest me what is going on here.
Thank you for your time.

Regards
Ranajit

2

Use the -noappend option and mdrun will not look for existing files.

3

Hello @jalemkul ,

Thank you for the help.
I have submitted with -noappend yesterday.
I was just being curious can we prepare a full trajectory in a single run?
Regards
Ranajit

4

You can run any simulation for as long as you like, depending on the queueing policies of the computer you’re using (if there are any).