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

Justin Lemkul jalemkul at vt.edu
Mon Oct 15 18:15:31 CEST 2012

On 10/15/12 11:45 AM, benjfitz wrote:
> As a further check I ran a neat solvent box and the simulation ends abruptly
> at 1.07 us.

These results suggest that your physical model is unstable.  A linear model of a 
triatomic species is not stable.  A more appropriate approach is to use virtual 
sites as in the following tutorial:


Also note that your cutoffs should not be dictated by your box size, rather the 
opposite should be true.  The cutoffs are an essential part of the force field 
model and changing them haphazardly can easily invalidate that force field model.



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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