[gmx-users] Parallel MD performance

[delara aghaie]

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?

Thanks
Regards
D.M



________________________________
 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

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

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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