[gmx-users] Semiisotropic Pressure coupling with PR

[Justin A. Lemkul]

Sai Pooja wrote:
> 
> 1. Pressure
> For my initial configuration, I run a long nvt run. This gives me a 
> pressure. Then I run an npt simulation at this prerssure. 
> 
> The idea is to do expansion runs(decrease pressure so that the system 
> expands) to get a P vs density curve. 
> 
> For example, after I determine the pressure of the initial configuration 
> from the long nvt run, say Pinit, I choose a set of pressures - Pinit, 
> P1, P2...., PN s.t Pinit>P1,>P2...(eg. 74, 72, 70, 69.....50). Then for 
> each pressure I run an npt simulation till the average converges.
> 
> 
> 2. Freeze-dimension
> Is there a better alternative for running simulations for a planar system?
> 

Maybe you want to use "pbc = xy" or walls?  Is there any literature precedent 
for what you want to do, or perhaps an alternate procedure?

-Justin

> 
> Pooja
> 
> On Thu, Jul 15, 2010 at 10:02 AM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 
> -- 
> Quaerendo Invenietis-Seek and you shall discover.

-- 
========================================

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

========================================