[gmx-users] pair interaction energy decomposition analysis

Justin A. Lemkul jalemkul at vt.edu
Tue Jun 19 20:37:41 CEST 2012

On 6/19/12 8:02 AM, Ngo Son Tung wrote:
> Dear Gromacs Users,
> I need calculate pair interaction energy decomposition analysis between
> Aromatic hydrocarbon ring and protein to discovery distribution of
> aromactic hydrocarbon ring of drug candidate in the interaction of ligand
> and protein. However, when I try to run MD with zero step from the complex
> structure that get from MD simulation by set:
> energygrps = protein ROU
> ROU is the atoms group of aromactic hydrocarbon ring that was define by
> index.ndx file, and I have error:
> atoms 389 and 391 in charge group 1 of molecule type 'LIG' are in
> different energy groups
> LIG is name of my non-protein compound.
> So, How I can fix this problem to calculate pair interaction energy
> decomposition between the aromactic hydrocarbon ring of ligand with
> protein?

Apparently your group ROU is set such that it breaks apart LIG into pieces that 
violate the requirement stated above in the error.  If two atoms are in the same 
charge group, they have to be in the same energygrp.  I suppose you can get 
around this with single-atom charge groups (but beware such things may or may 
not be right, depending on your force field) or by running your simulation in a 
normal way, then using mdrun -rerun to recalculate energies based on a dummy 
topology where you have broken the charge groups apart.  This may or may not be 
of some value.

Also realize the term "pair interaction" refers to an intramolecular interaction 
discussed in the manual, section 5.3.4.



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


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