[gmx-users] Extending the MD

[SAPNA BORAH]

:)

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

On Thu, May 26, 2016 at 6:01 PM, sun <sun.iba2 at gmail.com> wrote:

> Allright Sapna. Thank you very much.
>
> Sent from my iPhone
>
> > On 26-May-2016, at 4:59 pm, SAPNA BORAH <sapnauser365 at gmail.com> wrote:
> >
> > I would suggest if you want simulation runs with new name, add the
> -deffnm
> > switch and provide the default name :)
> > Saves us from all the trouble to rename the files all over again.
> >
> > gmx mdrun -v -s next1.tpr -cpi state.cpt -deffnm new
> >
> >
> > Sapna Mayuri Borah
> > c/o Dr. A. N. Jha
> > Research student
> > Tezpur University,
> > India
> >
> >> On Thu, May 26, 2016 at 4:57 PM, SAPNA BORAH <sapnauser365 at gmail.com>
> wrote:
> >>
> >> 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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