It might be worth noting that I am not sure the Amber12 compile available
on Stampede via "module load" is up to date with bug fixes. This could
especially cause problems with the GPU code if I'm not mistaken.
I'm still awaiting a response from the TACC staff on the matter.
Regards,
Brian
On Mon, Sep 9, 2013 at 5:42 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> > lines, respectively. The graduate student I work under informed me there
> > should be twice as many lines in the NVT.restrt file; however, it is
> three
>
> This is not strictly true. The Amber ASCII restart format is:
>
> Title line
> Natom [time] [temp0]
> <Natom * 3 Coordinates>
> [<Natom * 3 Velocities>]
> [Box Info]
>
> In your initial restart (presumably from a minimization) there is no
> velocity information, whereas in your MD restart you do have velocity
> information. Therefore the number of lines in the MD restart (M)
> compared to the number of lines in the Min restart (N) should be:
>
> M = ((N - 3) * 2) + 3
> M = 2N - 3
> (if you had no box info it would be M = 2N - 2)
>
> So the number of lines in your second restart appears fine (this of
> course doesnt preclude their being some other kind of problem with the
> restart). You could do some basic checking of the restart via the
> 'check' command in cpptraj.
>
> Your best bet when troubleshooting an error like this is to simplify
> the run as much as you can. So try running only a few steps (10-100)
> using the serial version of the code, printing out information every
> step. Sometimes error messages are harder to find when running
> multiple threads.
>
> Hope this helps,
>
> -Dan
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
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>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Tue Sep 10 2013 - 10:30:08 PDT
