[gmx-users] Re: how to turn off the interamolecular interaction

xianghong qi xianghong001 at gmail.com
Wed Nov 19 08:17:32 CET 2008

Yes, Mark. I now understand. I use united atom model. In my system, protein
includes only methane pair.  I still need those parameter to control
protein/solvent, solvent/solvent interaction. Thanks so much for your great
help.  I will do it now.

Best, -Xianghong Qi

On Wed, Nov 19, 2008 at 1:48 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> xianghong qi wrote:
>> Thanks, Mark.  That means I can set energygrp_excl = Protein Protein, then
>> I can get rid of  those parameter which are related to electrostatics, Vdw(
>> like rcoulomb, vdw-type, rvdw, rvdw-switch, etc).  Am I right?
> No. Section 7.3.19 indicates how this should be done. I think you want
> energygrp_excl = Methane1 Methane2
> so you will need to use make_ndx suitably to create these groups.
> If "Protein" includes only your pair of methanes, then
> energygrp_excl = Protein Protein
> will have the same effect, only because there are no intramolecular
> nonbonded interactions in methane. It's thus not a generalizable solution...
> Mark
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