[gmx-users] high pressure simulations

Ran Friedman r.friedman at bioc.uzh.ch
Thu Nov 15 14:19:47 CET 2007

Dear Mateusz,

You may be aware of that, but just in case: please note that the
forcefield parameters are usually developed with an ambient pressure in
mind. Both proteins and water change somewhat when a higher pressure is
applied. These changes involve e.g. equilibrium lengths of bonds and the
dielectric of water. Whether or not this has a significant effect on
your simulation depends on what you're actually studying.

As to your question, note that the isotermal compressibility also
changes with the pressure and you'll have to take that into account as
well. Maybe if you change only this parameter and keep tau_P to a value
that works in ambient pressure you'll be fine. You may also try to
increase the pressure gradually and equilibrate.


mateusz sikora wrote:
> Hi all,
> i am trying to set up high pressure simulations of a protein. I am
> using NPT ensemble, with isotropic pressure scaling, standard
> compressibility, room temperature. I am wondering how I can rise
> pressure from 1 bar to as much as 5 kBar. Is it safe to do it under
> Parinello-Raman coupling? I want to avoid huge oscillations of a box
> while adding the pressure - they can result in a box
> explosion/collapse. Would setting tau_P to some bigger value (like 100
> or something) make any difference?
> I appreciate any help
> Regards
> -- 
> Mateusz Sikora
> http://www.karakorum2008.e-gory.pl
> ------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Email: r.friedman at bioc.unizh.ch
Skype: ran.friedman

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20071115/bb466674/attachment.html>

More information about the gromacs.org_gmx-users mailing list