[gmx-users] Interaction energy between two molecules.

Justin Lemkul jalemkul at vt.edu
Mon Dec 3 05:11:37 CET 2012

On 12/2/12 10:38 PM, Mortuza Munna wrote:
> Dear Gromacs User, I am simulating two constrained fullerenes to analyze the
> interaction energy between these two in vacuum. To do that I specified
> energygrps in .mdp file as CB1 and CB2 which corrospond to the residue name
> of first and second fullerene respectively. The charge of the atoms of
> fullerenes are zero. Therefore, only the LJ-SR of CB1-CB2 should be the total
> interaction energy between these two. My understanding is, this total
> interaction energy is the combination of both attractive and repulsive term
> of Lennard-Jones potential. Is there anyway to find only the attraction
> energy (-C6/r^6) which is contributing to this total interaction energy
> between these two fullerenes? Or, in other words I would like to know the
> attractive energy (-C6/r^6) between these two fullerenes. I would really
> appreciate if anyone can help me.

The approach that comes to mind is to create a custom topology in which the 
relevant C6 or C12 parameters are alternatively set to zero.  You can then 
create new .tpr files that have either only attractive or only repulsive terms. 
  Then use the mdrun -rerun feature with this new .tpr file and the existing 
trajectory file to have the energies recalculated.



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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