[gmx-users] Extending the MD

[SAPNA BORAH]

Well that's kinda new i must say. Can you please paste the entire command
you have used. I think you have mis-named the file :).

By previous.cpt, I mean your last/previous checkpoint file of the
simulation run, that will be state.cpt in your case.. Hope you have
mentioned that. Ignore if you have :)

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

On Thu, May 26, 2016 at 4:38 PM, sun <sun.iba2 at gmail.com> wrote:

> Hello Sapna
> I tried adding previous.cpt but the following the following error appears:
> "One out of the 4 files is either missing or renamed"
>
>
>
> Sent from my iPhone
>
> > On 26-May-2016, at 4:35 pm, SAPNA BORAH <sapnauser365 at gmail.com> wrote:
> >
> > Hi!!
> >
> > After converting the tpr, while initiating mdrun, try adding the previous
> > cpt file as well..
> >
> > mdrun -s next.tpr -cpi previous.cpt
> >
> > Thanks!
> >
> >
> > Sapna Mayuri Borah
> > c/o Dr. A. N. Jha
> > Research student
> > Tezpur University,
> > India
> >
> >> 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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