[gmx-users] how to obtain binding energy?

Justin A. Lemkul jalemkul at vt.edu
Tue May 17 14:15:48 CEST 2011

shahab shariati wrote:
> Dear mohsen
> thanks for your reply.
> I forgot to say there are water and ion in my system.
> with new conditions, can I use PMF or TI?

You can use either.

> I have another question:
> is there this possibility to obtain affinity between protein and ligand 
> by gromacs? please guide me about that.

Do you mean binding constants?  If you obtain reliable DeltaG values, then apply 
standard thermodynamic relationships.



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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