Steven Neumann wrote:
Dear Gmx Users,
I would like to calculate the interaction energy (LJ and
electrostatic) between each residue and my ligands (10 ligands in the
system). I would like to see what is the contribution of electrostatic
and vdW interactions between ligand and each of my residue. I thought to
use g_energy and specify each of my residues in index files but it is
not possible. Will you suggest how to do this?
For such information, you have to specify these groups as energygrps in the .mdp
file. You can rerun the trajectory using mdrun -rerun and a new .tpr file
specifying these groups, but depending on the output frequency, the result may
not be as accurate as you'd like.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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