[gmx-users] Semiisotropic Pressure coupling with PR

[Justin A. Lemkul]

Sai Pooja wrote:

<snip>

>     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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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