[gmx-users] pause a run?

[Justin Lemkul]

On 3/23/18 11:16 AM, MD wrote:
> 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?

You're using incorrect syntax. -deffnm specifies the base name of all 
input and output files, so mdrun is going to go looking for md.tpr.tpr 
as input.

gmx mdrun -deffnm md -cpi -append

That's all you need.

-Justin

> 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
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>>

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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