----- Original Message -----
From: Hassan Shallal <hshal...@pacific.edu>
Date: Friday, July 2, 2010 17:40
Subject: [gmx-users] GBSA calculations
To: gmx-users@gromacs.org
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> 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...
Until the release of GROMACS 4.5, this will not be available. After that
release, it will surely be in the manual :-)
Mark
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