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 Cheers, Andrés 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 (UNLP-CONICET-CIC) 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: [EMAIL PROTECTED] web site: www.iflysib.unlp.edu.ar _______________________________________________ gmx-users mailing list [email protected] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
