[gmx-users] Re: energy group exclusions

Sikandar Mashayak symashayak at gmail.com
Tue Apr 19 06:57:17 CEST 2011

so that means if I define a index group GRP and energy exclusion GRP GRP
then all the non-boned interactions between atoms belonging to GRP group are

On Mon, Apr 18, 2011 at 7:43 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  On 4/18/2011 1:43 PM, Sikandar Mashayak wrote:
> Also, what about non-bonded interactions within the protein? Does exclusion
> group only exclude the non-bonded interactions between two different
> molecules and non-bonded interactions within the single molecule atoms are
> still computed?
> The sets of atoms for energy groups and such exclusions are defined by the
> index groups, not molecules. See manual 7.3 and wherever it talks about
> groups in an early chapter.
>  On Sun, Apr 17, 2011 at 10:38 PM, Sikandar Mashayak <symashayak at gmail.com
> > wrote:
>> Hi
>>  When we define energy group exclusions e.g. like in manual energygrp
>> excl = Protein Protein SOL SOL
>> and do md rerun, then only non-bonded interactions between Protein and SOL
>> are computed. I am wondering what happens to bonded interactions within the
>> protein, do they contribute to energies even though we have excluded
>> protein-protein interactions?
> Bonded interactions are unaffected, as you will see if you try it.
> Mark
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110418/4e723205/attachment.html>

More information about the gromacs.org_gmx-users mailing list