[gmx-users] high pressure simulations

Andrés N. McCarthy amccarthy at iflysib.unlp.edu.ar
Thu Nov 15 14:20:25 CET 2007

Hi Mateusz,
IMHO the berendsen Berendsen barostat is a better option to avoid introducing 
important oscillations in pressure.
For an alternatives on how to proceed with pressure scaling and equilibrating 
you might find useful to read through some of the following recent 
publications on the subject:

Effect of pressure on the conformation of proteins. A molecular dynamics 
simulation of lysozyme 
Journal of Molecular Graphics and Modelling 
Volume 24, Issue 4 , January 2006, Pages 254-261

Pressure denaturation of Apomyoglobin. A molecular dynamics simulation study.
Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics 
Volume 1764, Issue 3 , March 2006, Pages 506-515



On Thu 15 Nov 2007 09:48, 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


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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