On Mon, Oct 17, 2011 at 6:02 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > 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 > > Thank you Justin. Now I have two groups sepcified in my mdp file: energygrps = Protein LIG How can I specify each residue of my protein separately and each ligand? In my md.gro file I have residues: > 91GLY 92TYR ..... 161LIG 162LIG... Will it be correct like this energygrps = 91GLY 92 TYR ... 161LIG 162LIG... If yes, will this simulation take longer? Thank you Steven
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