[gmx-users] Parallel MD performance

delara aghaie d_aghaie at yahoo.com
Mon Jun 11 07:06:44 CEST 2012

Dear Gromacs users
I have checked something today and it seems starnge to me. Doing the Justin lyzozyme tutorial, I checked the performance of our parallel system. Subimitting the job on 8 processors of one node, I get0.86 ns/daywhich seems to be very weak performance. Do you have any idea about the ns/day performance of 8 processors for the same lyzozyme system?


 From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Sunday, 3 June 2012, 17:16
Subject: Re: [gmx-users] Atomtype 1

On 6/3/12 8:24 AM, xi zhao wrote:
> Dear gmx-users:
> I add a new residue in *rtp ,according to
> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field,
> and modified corresponding files :such as atp, hdb , after making a full copy of
> the installed forcefield in woring diectory.
> When pdb2gmx_d
> appeared "
> All occupancies are one
> Opening force field file ./amber99sbr.ff/atomtypes.atp
> Atomtype 1"
> Please give me suggestions

Did the program hang here?   Did it crash?  What modifications did you make, and to what files?  Are you using a plain text editor that properly treats newlines?


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

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

-- gmx-users mailing list    gmx-users at gromacs.org
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120611/354b69e4/attachment.html>

More information about the gromacs.org_gmx-users mailing list