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
--
========================================
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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