Best way for extending molecular dynamics simulation

User discussions
1

GROMACS version:2020.4
Hello everyone,

I want to ask to extend my molecular dynamics simulation. I’ve searched the forum before but I’ve seen different answers about this and I want to be sure before doing extended simulation.

I have a 1 µs long completed MD trajectory, I want to extend this simulation to 2 µs. I want to start the new simulation from the end of the first simulation, as a continuation. I also want to append the extended simulation to my previous simulation.

I’ve seen these two sets of commands for this:

1st:
(By editing tpr file)
gmx convert-tpr -s complex.tpr -extension 1000000 -o complex_new.tpr
gmx mdrun -deffnm complex_new -cpi complex.cpt -append

2nd:
(by editing the md.mdp file for 2µs simulation)
gmx grompp -f md.mdp -c complex.gro -p complex.top -o complex_new.tpr
gmx mdrun -deffnm complex_new -append -cpi complex.cpt

Which is the most reliable way? My simulations are too long and I hesitate to do anything wrong.

I’m waiting for your help.

Bests,

1 Like
2

Use convert-tpr. You only ever need to invoke grompp when you are changing something about the .mdp options. Note that the convert-tpr option is -extend, not extension.

1 Like
3

Thank you very much. Indeed, in the second command set includes changing mdp file and running the simulation from checkpoint.

gmx convert-tpr -s complex.tpr -extend 1000000 -o complex_new.tpr
gmx mdrun -deffnm complex_new -cpi complex.cpt -append

You recommend this one, thanks again.

4

Hi again,

I am not sure about appending the second simulation to the first one. In this command, I guess it is not possible because of -deffnm option.

I think appending the simulation as a continuation of the first part would be more useful for the analysis part, what do you suggest?

Thanks in advance

5

It doesn’t matter whether you append now or not. You can concatenate trajectory and energy files after the run if you don’t do it directly with mdrun.

6

Thank you very much. After this simulation, for whole part (previous 1µs simulation + extended 1 µs), how can I do image correction? Which tpr file should I use? First one (complex.tpr) or extended tpr (complex_new.tpr) file?

7

It doesn’t matter, the coordinates in both are the same.