[gmx-users] Re: for gromacs

Justin A. Lemkul jalemkul at vt.edu
Tue Oct 19 13:30:33 CEST 2010

As I say continually, I am not a private tutor.  Please keep all Gromacs-related 
correspondence on the gmx-users list.  I am CC'ing this message there and would 
ask that any further discussion be held in this forum.

Binding energy is not trivial to calculate, and will require some type of free 
energy calculation (thermodynamic cycles, potential of mean force, etc). 
Breakdown of short-range nonbonded terms can be accomplished by using the 
"energygrps" keyword in the .mdp file.  If you've already done your simulation, 
you'll have to use the mdrun -rerun function with a new .tpr file that has these 
groups defined.


rajender verma wrote:
> dear sir
>  I have done MD study of a complex compound (protein-Ligand). I want to 
> calculate the Binding and breakdown energy with protein- ligand. pllease 
> help me sir
> Thanks
> -- 
> Rajender Kumar
> Senior Research Fellow
> National Institute of Pharmaceutical Education and Research (NIPER),
> Sector - 67, S.A.S. Nagar. 160062, Punjab, INDIA
> http://bioinfoindia.weebly.com/


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


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