[gmx-users] Re: gormacs files for CG DNA

Justin A. Lemkul jalemkul at vt.edu
Fri Jan 23 22:00:31 CET 2009

Please keep all Gromacs-related correspondence on the users' list.

I do not have the time or resources to run jobs for you, nor do I typically open 
attachments that I did not request.  I did take a look at your structure file 
and script, however, and I can tell you this much: running a 74,000-atom system 
on a single core will take an *extremely* long time using version 3.3.1.  Thus, 
as I said before (twice), the problem is most likely that you are not waiting 
long enough.  Your simulations will be *very* slow.  If you only have access to 
a single CPU, then at the very least install version 4.0.3 (the most recent 
version) to try to get as much of a speed upgrade as you can.  Otherwise, you 
will be waiting for a very long time for MD results.


He, Yang wrote:
> Hi Justin,
> I will forward these gromacs files to you ,hoping you can help me figure out this problem.
> Thank you for your suggestions,
> Yang


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


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