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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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