On 11/6/12 9:01 AM, benjfitz wrote:
Thanks for the suggestion, I should have mentioned Tcoupl and Pcoupl in my
previous post. I changed them from Nose-Hoover/Parrinello-Rahman to
V-rescale/Berendsen and one permutation mixing the two, but it crashed all
the same.
The nodes have at least 8 GB of ram and free -m shows that I'm not running
out, even when it gets close to the magical 1.07 us. I'm currently running a
2 us NVT simulation with CS2 and PME. Do you have any other thoughts as to
options I can change to narrow this down? Perhaps a third coulombtype?
Thanks in advance.
Rather than run the entire job in one sitting, I would suggest running in
smaller chunks of time (e.g. 500 ns or so) and restarting from checkpoints as
necessary to reach the desired 2 us. It would be interesting to see if there is
some accumulated error that arises from a very long simulation that is mitigated
or fixed by using smaller increments of time.
-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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