[gmx-users] Re: energy group exclusions

Justin A. Lemkul jalemkul at vt.edu
Mon Apr 18 13:27:27 CEST 2011

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?

Nonbonded interactions are excluded between each defined pair.  Therefore, with

energygrp_excl = Protein Protein SOL SOL

you are excluding all nonbonded interactions between protein atoms (Protein 
Protein pair) and between solvent atoms (SOL SOL pair).  Protein-solvent 
interactions are calculated.  The use of energygrp_excl (as documented) 
indicates that only nonbonded interactions are affected.  That is, bonded 
energies should still be calculated for all groups.


> On Sun, Apr 17, 2011 at 10:38 PM, Sikandar Mashayak 
> <symashayak at gmail.com <mailto: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?
>     thanks
>     sikandar


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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