[gmx-users] Semiisotropic Pressure coupling with PR

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 15 16:02:51 CEST 2010

Sai Pooja wrote:


>     Do you run any equilibration prior to applying these parameters?
>      Both N-H and P-R allow for wide fluctuations in temperature and
>     pressure, respectively, which are exacerbated by systems that are
>     not sufficiently equilibrated.  Hence it could take a very long time
>     if you do not equilibrate well using, i.e. a weak coupling scheme first.
> I usually start with a pressure nearby. For example, I start with a 
> system which was equilibrated at p=71 and then run npt at p=69. Is that 
> not sufficient?

How do you determine the pressure before the simulation has begun?  Moreover, 
freezing your system in one dimension can certainly complicate matters, since 
that is a non-equilibrium restraint on the dynamics.  That could be a factor.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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