[gmx-users] Interaction energy

[Justin A. Lemkul]

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

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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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