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