Xavier Periole wrote:
On Wed, 05 Mar 2008 20:38:59 +0100 (MET)
[EMAIL PROTECTED] wrote:
Dear developers,
I would like to know the exact definition of the total potential
energy with
respect to protein-solvent interactions, in an explicit solvent
protein simulation.
The definition of protein-solvent interaction is the sum of the
pair-wise interaction (non-bonded) involving on one side the protein
atoms and on the other side the solvent atoms.
For protein atom Pm and solvent atom Wn, there are two interactions:
Pm to Wn
Wn to Pm
Those two terms are identical! You can not separate them! Here you just
express them in two different ways which are totally identical.
It is like A+B=B+A, can you differentiate the sum of B on A and the
sum of A on B?
Are both interaction energies counted in the total potential energy
given in the log file or by g_energy?
As they are the same they are both counted but only one time!
If I want to compute the total potential enery of the protein, plus
protein-solvent interactions, should I then only add half of the
protein-solvent terms given by g_energy? I am only interested in the
effect of solvent "felt" by the protein, and not in the effect of the
protein felt by the solvent.
Again, how would you differentiate those two terms? Counting
the interactions from protein to solvent or solvent to protein is
exactly the same.
Still, if you want to partition the energy over molecules you have to
make some kind of division. For instance, if you calculate the potential
energy for 216 water molecules you will find that is is roughly -9000
kJ/mol at room T, and hence you can derive the potential energy per
molecule to be -42 kJ/mol, which agrees with heat of vaporization. If
you however would do as you suggest, and take one water molecule and
compute all its intermolecular interactions you would end up with an
energy of -84 kJ/mol, because all terms are counted double! Therefore it
is entirely reasonable (though this is not a rigorous derivation!) to
partition the Protein-Solvent energy equal between protein and solvent,
in order to get an estimate of the Protein energy. As an extra
indication that this is reasonable, the linear interaction energy method
by Aqvist (Prot. Eng. 7 (1994) p. 385-391) derives that the contribution
to the Gibbs energy of solvation involves 0.5 times the protein-solvent
Coulomb interaction.
A proper derivation would probably involving computing the heat of
solvation for the protein, and compare that to potential energies that
come directly from the simulation, (and obviously to experimental data).
Cheers,
--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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