[gmx-users] Re: how to turn off the interamolecular interaction
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...
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Some people make the world more special just by being in it.
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users