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

[Alex]

Sorry, didn't notice the cpt files weren't yet generated. Justin is 
always right about everything.

Alex

On 12/29/2016 1:58 PM, Zhang, Cheng wrote:
> 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
>
>
>