On 2012-01-19 14:49, Ivan Gladich wrote:
On 01/19/2012 11:34 AM, Steven Neumann wrote:
Does anyone can help?
Dear Gmx Users,
I am wondering whether it is possible to obtain in Gromacs chemical
potential e.g. of water in the protein - ligand system?
Please, advise me to do some further reading, suggest method, maybe
tutorial?
Thank you,
Steven
Dear Steven
I am not an expert of protein - ligand system...
However the chemical potential of a i-th specie is the derivative of the
potential energy in function of the number of the i-particles present in
the system.
As far as I know (and if I am not wrong), in GROMACS the number of
particle is fixed along all the simulation, i.e., you cannot change the
number of particles during the simulation.
Therefore, you cannot simply obtain the chemical potential from one
single run...
I suggest you to search in literature; maybe you can combine different
runs to obtain the chemical potential...but I do not want to say you
something wrong since I do not have experience in such systems.
Good luck
Ivan
Correct me if I'm wrong, but in principle you can just do an
annihilation simulation in solution and the free energy obtained in this
manner is the chemical potential. If you do the same in the gas phase
and subtract that you get the Gibbs energy of hydration.
--
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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