Xavier Periole wrote:
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?
There are no terms calculated double in the MD simulation. But the
average interaction energy is indeed -84 kJ/mol.
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!
Hm, what can I say? We are actually working on testing something like
this systematically, i.e. how does the energy of a protein/water system
changes with the number of water molecules, no results yet though.
--
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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