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.
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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