[gmx-users] Re: Error in npt run - box size/ triclinic skew factor

Justin Lemkul jalemkul at vt.edu
Wed Oct 31 17:42:04 CET 2012

On 10/31/12 12:38 PM, mtso wrote:
>> Just make sure whatever changes you are making are correct for the chosen
> force
>> field and algorithms.  If you're having problems with NPT, you can always
> switch
>> to the Berendsen algorithm for pressure coupling before returning to
>> Parrinello-Rahman for data collection.
> -Justin
> Thanks for the quick response, I've changed to the Berendsen algorithm, and
> still get the same error message.  When looking at the files we've used in
> the past for similar simulations, the file we use for annealing has pressure
> coupling off.  Would it even be necessary to do NPT before annealing then?

You didn't mention annealing before, that would have been helpful to know.  So 
the .mdp file you posted before is not one that is causing a problem?  I'm just 
lost as to what you're doing now.  Doing annealing using NPT may become 
unstable, depending upon how happy the system is to start and how drastic the 
temperature changes are.  NVT is probably more stable for annealing.



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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