[gmx-users] How to extend my incompleted simulation? (not extend a completed one)

[Zhang, Cheng]

Hi Justin,

Thank you very much. It worked as you said [😊]


Yes, I was only using 10 min in the beginning, so no cpt file could be generated.


Yours sincerely

Cheng

________________________________
From: Zhang, Cheng
Sent: 29 December 2016 19:02:47
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: How to extend my incompleted simulation? (not extend a completed one)


Hi Alex,

Thank you. I tested "mdrun_mpi -deffnm md_0_1 -cpi state.cpt -append". However, I still ONLY got the four files WITHOUT cpt file.

) md_0_1.trr
) md_0_1.xtc
) md_0_1.edr
) md_0_1.log


I know the link http://www.gromacs.org/Documentation/How-tos/Extending_Simulations,

but is it for extending a completed job? In my case, I want to continue a incompleted job.


Thank you.


Yours sincerely

Cheng


________________________________
From: Zhang, Cheng
Sent: 29 December 2016 18:23
To: gromacs.org_gmx-users at maillist.sys.kth.se
Cc: Zhang, Cheng
Subject: How to extend my incompleted simulation? (not extend a completed one)

Dear Gromacs,
I would like to extend my simulation.

200 ns was put in the "md.mdp" file, which was used to build "md_0_1.tpr".

Then, I use "mdrun -deffnm md_0_1" to submit "md_0_1.tpr".

Due to the limitation on our cluster, only 5 ns (for example) was simulated when the job finishes. The "md_0_1.tpr" file is NOT changed, and I got other new files but WITHOUT a cpt file (why?):
) md_0_1.trr
) md_0_1.xtc
) md_0_1.edr
) md_0_1.log

So I want to continue the simulation from the end of 5 ns. How should I do this?

I am not quite sure if I understand correctly from http://www.gromacs.org/Documentation/How-tos/Extending_Simulations, and I also feel this link does not address my problem, as the tpr file was not changed in my case.

Thank you.

Yours sincerely
Cheng