[gmx-users] Extending umbrella sampling window

Steven Neumann s.neumann08 at gmail.com
Mon Apr 23 19:59:03 CEST 2012


On Mon, Apr 23, 2012 at 6:45 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/23/12 1:38 PM, Steven Neumann wrote:
>
>> Dear Gromacs Users,
>>
>> My job failed on the cluster and I would like to run in from the
>> checkpoint time
>> created:
>>
>> mdrun -s umbrella0.tpr -cpi umbrella0.cpt -deffnm umbrella0 -pf
>> pullf-umbrella0.xvg -px pullx-umbrella0.xvg
>>
>> Will existing files pullf-umbrella0.xvg  and pullx-umbrella0.xvg be
>> updated as
>> the command for the initial run is:
>>
>> mdrun -s umbrella0.tpr -deffnm umbrella0 -pf pullf-umbrella0.xvg -px
>> pullx-umbrella0.xvg
>>
>>
> I see no reason why they wouldn't be.  Is there some problem when
> executing the appending run?
>
> -Justin
>


I am using 4.5.4. and -append is default. I am curious because I submit a
script and only 3 out 6 files are copied back to my working directory,
everything else is lost as only in temporary directly jobs can be run. No
clue what is happening.

Steven

>
> --
> ==============================**==========
>
> 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<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<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120423/ad8ee7b2/attachment.html>


More information about the gromacs.org_gmx-users mailing list