[gmx-users] high pressure simulations

Andrés N. McCarthy amccarthy at iflysib.unlp.edu.ar
Thu Nov 15 16:06:17 CET 2007

Taking up from Mark's comment, you might want to pay special attention to what 
water model you use; i.e. make sure it reproduces some experimentally well 
determined behaviour, such as the "anomalous" autodiffusion coefficient 
maximum (roughly around 2kbar for pure water at 300K).




On Thu 15 Nov 2007 10:17, Mark Abraham wrote:
> 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?
> Changing tau_p will damp the extent to which the coupling affects the
> system. You should probably do this process with stepwise increments of
> ref_p. You should also go and parameterize a force field for high
> pressures, too, since the standard ones are parameterized against
> experimental data from 1 bar or so. There's no reason to suppose the
> parameters are transferable to high pressure, unless you can demonstrate
> that they are by comparison of simulation and suitable experimental data.
> Mark
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Dr. Andrés N. McCarthy
Instituto de Física de Líquidos y Sistemas Biológicos
Depto. Cs. Biológicas - Fac. de Cs. Exactas - Univ. Nac. de La Plata
59-789, CP (1900) La Plata, Argentina
Tel: +54-221-4254904 / +54-221-4233283
FAX: +54-221-4257317
e-mail:     amccarthy at iflysib.unlp.edu.ar
web site:   www.iflysib.unlp.edu.ar

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