[gmx-users] Advantage of NPT over NVT?

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Oct 13 12:48:57 CEST 2009


Hi,

In addition to the remarks of Ran and Mark, also note that with NVT
the density of your system may change significantly and artificially,
relating to changes in your protein. This in turn affects the dynamics
of your protein, which should be considered an artefact of NVT
simulations.

Cheers,

Tsjerk

On Tue, Oct 13, 2009 at 8:46 AM, Ran Friedman <r.friedman at bioc.uzh.ch> wrote:
> Hi,
>
> The simplest ensemble is NVE. Historically, NVT came later to allow
> simulations in constant temperature which seem to be more realistic from an
> experimental point of view. However, experiments are usually performed under
> constant pressure and temperature, which is the reason for people to choose
> NPT.
>
> Parameters that deal with a thermostat and barostat are not straightforward
> to choose - there have been a lot of posts on this list about it. Even NVT
> is not simple.
>
> Ran.
>
> --
> ------------------------------------------------------
> Ran Friedman
> Postdoctoral Fellow
> Computational Structural Biology Group (A. Caflisch)
> Department of Biochemistry
> University of Zurich
> Winterthurerstrasse 190
> CH-8057 Zurich, Switzerland
> Tel. +41-44-6355559
> Email: r.friedman at bioc.unizh.ch
> Skype: ran.friedman
> ------------------------------------------------------
>
> Pan Wu wrote:
>
> Hello everyone,
>     Is there any advantage of using NPT ensemble over NVT? Seems people
> doing simulation with gromacs like to use NPT (for protein + solvent
> system). However, for NPT, there is one parameter "compressibility" which is
> tricky to choose; for NVT, it is so simple.
>     Can anyone give me some suggestion or explanation on this part?
>     Thank you very much in advance!
> Sincerely
> Pan Wu
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623



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