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: yel...@uni-mainz.de
> To: gmx-users@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-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
> Of Berk Hess [g...@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.h...@mytum.de
> > To: gmx-users@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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