[gmx-users] Semiisotropic Pressure coupling with PR
Justin A. Lemkul
jalemkul at vt.edu
Thu Jul 15 16:21:12 CEST 2010
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?
> 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:
> 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
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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