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

[Mark Abraham]

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