[gmx-users] Extending the MD

[SAPNA BORAH]

It may be a case. You can rename the files to what they were and try again.
Since here, the error simply implies the files are renamed or missing.

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

On Thu, May 26, 2016 at 4:46 PM, sun <sun.iba2 at gmail.com> wrote:

> Yes
> In my case it was state.cpt and used the following command after
> generating .tpr:
> gmx mdrun -v -s next1.tpr -cpi state.cpt
>
> Has it anything to do with trajectory or log files generated in 100 ns
> case? I have renamed the .trr and .xtc files generated for 100 ns
> simulation.
>
> Sent from my iPhone
>
> > On 26-May-2016, at 4:43 pm, SAPNA BORAH <sapnauser365 at gmail.com> wrote:
> >
> > 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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