[gmx-users] interaction energy

Justin Lemkul jalemkul at vt.edu
Sun Mar 30 23:57:18 CEST 2014

On 3/30/14, 12:03 PM, pratibha wrote:
> Thank you Justin for your reply.
> When I include MainChain+H Sidechain LIG as my energygrps in *.mdp file
> (This is what I understand from specifying them as separate groups, please
> correct me if I am wrong) , I am getting following error:
> atoms 18 and 19 in charge group 7 of molecule type 'Protein_A' are in
> different energy groups
> How to rectify it?

Pairwise decomposition of energy groups requires that those groups be continuous 
with respect to charge groups.  If that's not the case, you can't decompose 
those energy groups.  You can almost certainly create custom groups that satisfy 
the requirements of the code.  It's just a simple matter of going into the 
topology and identifying instances like this one (which is labeled in every 
meaningful way so you can find it) and creating a suitable group.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


More information about the gromacs.org_gmx-users mailing list