[gmx-users] Enthalpy and energy questions on a solvated protein
David van der Spoel
spoel at xray.bmc.uu.se
Wed Mar 2 18:29:37 CET 2016
On 02/03/16 16:28, Juan José Galano Frutos wrote:
> Hi dear all:
> I'm trying to obtain the deltaH (enthalpy = potential energy + pV) in a
> given molecular process, so for that I'm drawing the enthalpy values of my
> systems (a small protein conveniently solvated and neutralized) from using
> gmx_energy on the .edr files.
> Then, my questions and reflexions are:
> Are the enthalpy or energy values I'm here obtaining actually reliable in
> terms of experimental real values taking into account I'm using the pretty
> rigorous CHARMM27 force field??
> My doubts here come up given that I'm obtaining values for my systems in a
> 10 to the 6 kJ/mol order (e.g -1 155 621 kJ/mol), which seems to me
> excessively high.
> I know, of course, these enthalpy or energy values strongly depend on the
> amount of solvent you have in your system, and I have done some tests in
> order to verify how is the variation of these energies in relation with the
> number of water molecules solvating my protein.
> But, what I wouldn't expect here is that such energy and enthalpy values
> were varied in about a 10 to 4 or 10 to the 5 order in simulation replicas
> carried out on my solvated protein. See the following data:
> replica Ave Enthalpy (kJ/mol)
> 1 -1161980
> 2 -1142910
> 3 -1217530
> Believe you that these significant changes are a normal variation of these
> energies in my simulations taking into account the system is exactly the
> same (just gen_seed in the velocity options was different)??
Enthalpies converge very slowly, especially in a complex system. If you
do three replicas of a system like that you probably need at least 500
ns per simulation. Then if you want to monitor differences (absolute
energies are meaningless so far in classical MD), you need to control
the error bars, which may mean even longer simulations.
> Any suggestion to obtain reliable enthalpy values in the event the results
> I'm getting are really senseless???
> Thanks a lot.
> Juan José Galano Frutos
> Department of Biochemistry and
> Molecular and Cellular Biology,
> Faculty of Sciences,
> University of Zaragoza
> Pedro Cerbuna # 12, 50009
> Zaragoza (Spain)
> +34 976 76 28 06
> Institute for Biocomputation and
> Physics of Complex Systems (BIFI)
> Mariano Esquillor, Edificio I + D - 50018
> Zaragoza (Spain)
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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