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

xianghong qi xianghong001 at gmail.com
Wed Nov 19 08:51:48 CET 2008

Hi, Mark:

I made the index file and call two methanes as methane1 and methane2 , then
I set energygrp_excl = methane1 methane2, but when I run grompp, it said
methane1 is not an energy group. What do you understand this problem?
Thanks. -Xianghong Qi

On Wed, Nov 19, 2008 at 2:17 AM, xianghong qi <xianghong001 at gmail.com>wrote:

> 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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