[gmx-users] Total potential energy: 1/2 protein-solvent interactions??
X.Periole at rug.nl
Thu Mar 6 10:38:51 CET 2008
On Thu, 06 Mar 2008 09:42:09 +0100
David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> Xavier Periole wrote:
>> On Wed, 05 Mar 2008 20:38:59 +0100 (MET)
>> pascal.baillod at epfl.ch 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!
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
>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!
>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).
> 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.
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
>or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
More information about the gromacs.org_gmx-users