[gmx-users] Extending the MD

[SAPNA BORAH]

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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