Hi together, > You have to make sure that you do not calculate forces between frozen atoms,
is it enough to include in grompp.mdp such command: ; Non-equilibrium MD stuff freezegrps = S freezedim = Y Y Y ;Energy group exclusion for position restraints energygrps = A S energygrp_excl = S S Or it excludes only energy calculations, but not forces? Regards, Leonid ________________________________________ From: [email protected] [[email protected]] On Behalf Of Berk Hess [[email protected]] Sent: Thursday, August 27, 2009 2:59 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] Pressure for froozen atoms Hi, Gromacs does not do anything special for frozen atoms. You have to make sure that you do not calculate forces between frozen atoms, if you want the virial to be correct. Berk > Date: Thu, 27 Aug 2009 14:46:47 +0200 > From: [email protected] > To: [email protected] > Subject: [gmx-users] Pressure for froozen atoms > > Hi guys, > > does gromacs use the following scheme to calculate the virial/pressure > for systems including froozen atoms: > http://www.ccp5.ac.uk/infoweb/wsmith22/wsmith22/wsmith22.html > ?? > > Thx, > Alex > _______________________________________________ > gmx-users mailing list [email protected] > http://lists.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 ________________________________ See all the ways you can stay connected to friends and family<http://www.microsoft.com/windows/windowslive/default.aspx> _______________________________________________ gmx-users mailing list [email protected] http://lists.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
