[gmx-users] pressure coupling and running MD

[Tsjerk Wassenaar]

Hi Ninoo,

With constant volume, you may get differences in the solvent density over
time, which can affect the domain motion. Probably you're better off with
pressure coupling.

Tsjerk

On 2/10/06, Yang Ye <leafyoung81-group at yahoo.com> wrote:
>
> Volume change or pressure change is not a primary issue. Grab a modeling &
> simulation book to know the difference in NPT and NVT. Also refer to
> papers
> in this field.
>
> > -----Original Message-----
> > From: gmx-users-bounces at gromacs.org [mailto:
> gmx-users-bounces at gromacs.org]
> > On Behalf Of ninoo mani
> > Sent: Friday, February 10, 2006 4:21 PM
> > To: gmx-users at gromacs.org
> > Subject: [gmx-users] pressure coupling and running MD
> >
> > Dear gmx users
> > I want to study domain movement in proteins using.
> > I want to know whether I should use pressure coupling
> > along with temperature coupling or not. As some of you
> > mentioned before if I couple pressure volume will
> > change to adjust pressure (NPT) but if I do not couple
> > pressure volume will remain constant and pressure will
> > change (NVT). Since I want to study domain motion
> > which one would be better although I do not think for
> > this study it should make much of difference. I it
> > does not make difference which condition imposed more
> > often.
> > thanking in advance.
> > Ninoo
> >
> >
> >
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--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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