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. Ran. 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 [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 -- ------------------------------------------------------ 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: [EMAIL PROTECTED] Skype: ran.friedman ------------------------------------------------------
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