On Thu, 06 Mar 2008 09:42:09 +0100
David van der Spoel <[EMAIL PROTECTED]> wrote:
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.
Agreed.
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!
There no terms counted 2 times in this calculation!? They become doubled if
you use this number x 216 H2O to obtain the total potential energy. The
average interaction energy of one molecule with 215 others is still -84
kJ/mol!
Isn't it?
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.
I totally miss the concept of partitioning the interaction energy between
two parts into each one!
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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-----------------------------------------------------
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------
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