[gmx-users] Extending the MD

SAPNA BORAH sapnauser365 at gmail.com
Thu May 26 13:05:37 CEST 2016


After converting the tpr, while initiating mdrun, try adding the previous
cpt file as well..

mdrun -s next.tpr -cpi previous.cpt


Sapna Mayuri Borah
c/o Dr. A. N. Jha
Research student
Tezpur University,

On Thu, May 26, 2016 at 4:31 PM, sun <sun.iba2 at gmail.com> wrote:

> Hello
> I started a 100 ns ns pro-lig simulation which was terminated accidently
> at 53.33 ns. Then I restarted simulation with checkpoint file and
> simulation ended at 100 ns. Now I have the md_0_1.tpr and next.tpr files
> which were generated for 53.33 and 100 ns data reapectively and log, trr
> file for both 53.33 and 100 ns MD. I have state.cpt, state_prev.cpt,
> md_0_1.cpt. Now i want to extend the simulation upto 200 ns. So i gave the
> following commands:
> gmx convert-tpr -f md_0_1.tpr -extend 200000 -o next1.tpr
> and
> gmx mdrun -v next1.tpr
> But, the mdrun started from initial step and time 0.00. That means
> simulation is starting from begining and not after 100 ns to 200 ns. I am
> confused if i am using the right .tpr file or shall I use checkpoint file.
> Same results are obtained when i used next.tpr instead of md_0_1.tpr. When
> i used checkpoint files (all three files in three different steps) the
> simulation is starting from 53.33 ns. Plz suggest where I am going wrong.
> With Regards
> Suniba
> Sent from my iPhone
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