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).
Cheers. Andrés 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 > _______________________________________________ > 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 -- 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
