[gmx-users] Enthalpy and energy questions on a solvated protein

Juan José Galano Frutos juanjogf at gmail.com
Wed Mar 2 16:28:07 CET 2016

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)??

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)

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