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

[Ehud Schreiber]

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
applications.

What do you think?

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

Hi Mohsen,

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

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

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

Sander


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?