[gmx-users] Interaction energy

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 17 19:02:04 CEST 2011

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list