[gmx-users] pause a run?

Smith, Micholas D. smithmd at ornl.gov
Fri Mar 23 16:21:52 CET 2018


Try the explicit command:

gmx mdrun -s md.tpr -cpi md.cpt -c (your configuration_outfile_here) -o (your trajectory file here) -e (your energy file here) -cpo md.cpt -v -g (your log file here)



===================
Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of MD <refmac5 at gmail.com>
Sent: Friday, March 23, 2018 11:16 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] pause a run?

So I killed one of my runs, then I used the "-cpi" command and tried this
" gmx mdrun -deffnm md.tpr -cpi md.cpt". But it was asking for file
"topol.tpr", which I don't have.. any help?
Thanks,
MD

On Fri, Mar 23, 2018 at 10:41 AM, MD <refmac5 at gmail.com> wrote:

> ​You mean I could use the md.cpt to re-run it?​
>
> On Fri, Mar 23, 2018 at 10:35 AM, Smith, Micholas D. <smithmd at ornl.gov>
> wrote:
>
>> If you are writing state files, you can just kill the jobs and use them
>> to restart.
>>
>> ===================
>> Micholas Dean Smith, PhD. MRSC
>> Post-doctoral Research Associate
>> University of Tennessee/Oak Ridge National Laboratory
>> Center for Molecular Biophysics
>>
>> ________________________________________
>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of MD <
>> refmac5 at gmail.com>
>> Sent: Friday, March 23, 2018 10:33 AM
>> To: gmx-users at gromacs.org
>> Subject: [gmx-users] pause a run?
>>
>> Hi Gromacs Folks,
>>
>> I was running 6 md runs at the same time (not super fast computer, so it
>> could take 3 months to complete based on rough estimation). However, I
>> need
>> to prioritize two runs now but I don't want to just kill the other 4 since
>> it has been several weeks since I started the runs.
>>
>> I wonder if there is a way I could "pause" the other 4 runs at this point?
>>
>> Thanks a bunch,
>>
>> MD
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
>
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.


More information about the gromacs.org_gmx-users mailing list