[gmx-users] check point file corrupted - umbrella sampling

[Poojari, Chetan]

Hi Justin,

Except for cpt i think rest of the command should be alright. 

For outputting cpt file and using it for extending runs, i must have used -cpo and not -o flag.


Kind Regards,
chetan
________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at vt.edu]
Sent: 20 September 2011 15:05
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] check point file corrupted - umbrella sampling

Poojari, Chetan wrote:
> Hello Justin,
>
> Thank you very much for your reply.
>
> I must hav used -cpo 0.cpt instead of -o 0.cpt.
>

Are you saying the commands shown below are wrong?  Using "-cpo 0.cpt" is indeed
the correct approach.

-Justin

>
> Kind Regards,
> chetan
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at vt.edu]
> Sent: 20 September 2011 14:44
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] check point file corrupted - umbrella sampling
>
> Justin A. Lemkul wrote:
>>
>> Poojari, Chetan wrote:
>>> Hello Chris,
>>>
>>> I followed the steps as mentioned in the umbrella sampling tutorial in
>>> gromacs.
>>>
>>> After NPT equilibration step, i did the umbrella simulation runs.
>>> Below are the commands which i used:
>>>
>>>
>>> grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top -n
>>> index.ndx -o umbrella0.tpr
>>>
>>> mdrun -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg -s umbrella0.tpr
>>> -o 0.cpt -c 0.gro -x 0.xtc
>>>
>>>
>>> So, I had 24 such commands in my job submission script (one script i
>>> had all the grompp command and in other script i had mdrun command)
>>> for 24 windows, which  gave me 24 cpt files.
>>>
>>> After the  final 24th window run, along with the output names
>>> specified by me it also outputted default gromacs file names
>>> state_prev.cpt, state.cpt, md.log, ener.edr.
>>>
>>> Please can I know if its necessary to output even log files for these
>>> 24 windows.
>>>
>>> Size of the  state.cpt or the other cpt files which i got during npt
>>> equilibration are 1.2 MB (these cpt files are okie when i do gmxcheck,
>>> it does not give any error), where as of 24 different cpt files, each
>>> has file size of 715MB. I had run simulations for 10ns on each window.
>>>
>> Your command specifies "-o 0.cpt" so that's the problem.  The file 0.cpt
>> is not a checkpoint, it is a trajectory.  The -o flag produces a .trr file.
>>
>
> More correctly, 0.cpt is not a *single* checkpoint, but rather a trajectory of
> checkpoints, and though -o can produce such an output, it is typically reserved
> for .trr output.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> ------------------------------------------------------------------------------------------------
> ------------------------------------------------------------------------------------------------
> Forschungszentrum Juelich GmbH
> 52425 Juelich
> Sitz der Gesellschaft: Juelich
> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
> Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher
> Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
> Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
> Prof. Dr. Sebastian M. Schmidt
> ------------------------------------------------------------------------------------------------
> ------------------------------------------------------------------------------------------------
>

--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================
--
gmx-users mailing list    gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists