[gmx-users] RE: Gibbs free energy of binding

Ehud Schreiber schreib at compugen.co.il
Thu Oct 21 10:39:03 CEST 2010

Actually, I believe that using the energy difference, Delta E, as an
approximation to the free energy difference, Delta G, is a valid
approach (which I'm considering myself). The entropic contribution to
Delta G, namely -T Delta S, may be less prominent than Delta E.
In addition, Delta S can be approximated by various means - see e.g.
Doig & Sternberg 1995. I understand that such an approach is utilized in
the Accelrys Discovery Studio.
Obviously, this is an approximation that might be too crude for some

What do you think?


On Oct 21, 2010, at 09:25 , Sander Pronk wrote:

Hi Mohsen,

The mean energy difference is only one component of the free energy

Before you go any further I'd suggest reading a good book on molecular
simulations, like 'Understanding Molecular Simulations' by Frenkel and

There's a good reason free energy calculations cover over half of that


On Oct 21, 2010, at 09:18 , mohsen ramezanpour wrote:

> Dear Justin
> If I do  two  MD simulations for a short time in the same
conditions(of course separately for protein and drug)
>  and calculate total energy of each one and sum them with each other
as E1 as nonbonding free energy of system.
> then a MD simulation for Protein-drug system in the same condition and
calculate it's total energy too as E2 as bound system .
> what does (E1-E2)mean?
> I think it is binding free energy,Is not it?
> in the other hand when we are working on NPT ensamble it means Gibbs
free energy is the main energy and our total energy is equal to Gibbs
free energy.
> Then,what is the problem?

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