[gmx-users] Re: Error: The Y-size of the box times the triclinic skew factor is smaller than the number of DD cells times the smallest allowed cell size

Justin Lemkul jalemkul at vt.edu
Tue Feb 12 23:46:18 CET 2013

On 2/12/13 5:44 PM, Sonia Aguilera wrote:
> Thank you Justin,
> So, your advice is not to perform the npt calculation and to run the md
> after the nvt?

A common mistake is to think that there is a "standard" protocol that one must 
follow.  While it is true that for the condensed phase, a common procedure 
involves restrained NVT and NPT prior to production simulations under an NPT 
ensemble, this protocol is by no means necessary or appropriate under all 
conditions.  Simulating in vacuo requires different procedures and .mdp 
settings.  This topic has been discussed several times just in the last week or 
two; please refer to the list archive for useful information.



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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