[gmx-users] Pressure for froozen atoms

Yelash, Dr. Leonid yelash at uni-mainz.de
Thu Aug 27 16:13:42 CEST 2009

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?


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


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.


> 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
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