[gmx-users] Re: Membrane Runs Crashing

Justin Lemkul jalemkul at vt.edu
Thu Jun 27 03:20:53 CEST 2013

On 6/26/13 8:39 PM, Neha wrote:
> Hi everybody,
> My runs keep crashing despite energy minimisation and fiddling around with
> nstlist values. I have been looking in the Gromacs manual particularly the
> interaction ranges in the domain decomposition section, which mentions that
> simulations can stop with error messages about missing interactions and
> atoms moving too far. It says the interaction between two and multi body
> bonded (rmb) is set based on the initial configuration automatically. Is
> there a way that I could see what Gromacs is using as those values after the
> simulation crashes?

Not after the crash, but you can see the initial DD setup in the .log file.

> I am thinking of using -rdd to change that number and see whether the
> simulation is more successful, although it will most likely be slower.

Worth a shot.

> Please let me know where I can get that information! I am getting frustrated
> with all these crashing runs.

I seem to recall a similar problem that someone reported a while back.  Since CG 
systems have bonded interactions over longer distances than atomistic 
simulations, the DD setup may not work quite as well.  Either try increasing 
-rdd or simply decreasing the number of processors you are using to create 
larger DD cells.  Doing so should improve the odds that cells do not resize such 
that they lose track of bonded information.



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


More information about the gromacs.org_gmx-users mailing list