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

David van der Spoel spoel at xray.bmc.uu.se
Thu Oct 21 10:45:21 CEST 2010

On 2010-10-21 10.39, Ehud Schreiber wrote:
> 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.

As a simple example the hydrophobic effect at room temperature is 
largely due to the entropy of the water [ at high temp it is due to the 
enthalpy of the water ].

Since the hydrophobic effect is involved in all ligand binding it seems 
quite hopeless to get any reliable numbers when neglecting entropy. No 
referee will buy that - I wouldn't.

> 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
> 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?

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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