[gmx-users] GBSA calculations
hshallal at PACIFIC.EDU
Fri Jul 2 09:38:57 CEST 2010
Dear Gromacs users,
I am running some simulations of ligand protein systems using GBSA option for the implicit solvent.
In an MM/GBSA model, there is this equation:
G(molecule) = G(solvations) + Egas - TS(solute)...
G(molecule) is the total free energy of solute
G(solvations) is the solvation free energy
Egas is the moelcular mechanical energy of the molecule summing up the electrostatic interactions, van der Waal contributions and the internal strain energy
TS(solute) is the sum of TS(trans), TS(rot), and TS(vib)
How can derive such a calculation from the input of my Gromacs simulation...
I looked in the mailing list, there were a couple of inquiries about this issues without reponses.
I know those calculations can be run through Amber which I don't have an access to, so first question is, can I execute those calculations from the Gromacs simulation output files like from the .edr for example? and if yes, any hint or reference on how to do this would be greatly appreciated...
University of the Pacific
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