[gmx-users] Re: Diatomic in MeCN NPT (NH and PR) simulation segfaults after 1 us

Justin Lemkul jalemkul at vt.edu
Tue Nov 6 15:25:29 CET 2012

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


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