[gmx-users] Pressure for froozen atoms

[Berk Hess]

That's enough for the non-bonded interactions.
Energy group exclusions work on both the energy and the forces.
But if you have bonded interactions between atoms in S you also need to exclude those.
Note that this only matters if you want to have the pressure.

Berk

> From: yelash at uni-mainz.de
> To: gmx-users at gromacs.org
> Date: Thu, 27 Aug 2009 16:13:42 +0200
> Subject: RE: [gmx-users] Pressure for froozen atoms
> 
> 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: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Berk Hess [gmx3 at hotmail.com]
> 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: alexander.herz at mytum.de
> > To: gmx-users at gromacs.org
> > 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 gmx-users at gromacs.org
> > 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 gmx-users-request at gromacs.org.
> > 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    gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

_________________________________________________________________
Express yourself instantly with MSN Messenger! Download today it's FREE!
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090827/46304c4b/attachment.html>