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

Justin Lemkul jalemkul at vt.edu
Wed Oct 31 15:25:36 CET 2012

On 10/31/12 10:23 AM, mtso wrote:
> Thanks Justin,
> We're using the tutorial, and those .mdp files as a starting point but
> actually running the simulations on the protein PDB ID 2LFM, without adding
> a ligand for now, and modifying the .mdp files as necessary.

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


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