I am extending a gromacs simulation from 100ns to 500ns, if I used a different -deffnm file name, will the generated trajectory file be complete and extended (i.e. 500ns) or will it be as if it's a new trajectory with 400 ns?
I want to keep the previously generated files and have the files of the restart with different names.
I think if you increase the time in the production.mdp file, rerun the gmx grompp command (to make a corresponding md.tpr file which conforms to the new timesteps ;500ns) followed by this command, “$ gmx mdrun -s md.tpr -cpi md.cpt -v -deffnm md -append” it will continue from where it stopped (as it reads from the checkpoint)…
As I understand your purpose of Q, you want to extend your simulation with the same md.mdp parameters in your 100ns. You can follow these recipes: 1- gmx convert-tpr -s previous.tpr -extend ( time to extend by picosecond) -o next.tpr 2- gmx mdrun -v -deffnm next ( from new .tpr file) -cpi (md prev.cpt) -noappend * -noappend option differentiates extended trjectories from primary ones.
* After termination you can cat your 100ns trj with 400ns trj = 500ns trj
@Justin Lemkul
The safest way to do it:
1) generate a .tpr file and run it
2) after finishing the extended simulation, just merge all trajectory files by means of trjcat command
3) you can easily use trajectory files to analyze your system
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