[gmx-users] RF and TI

Berk Hess gmx3 at hotmail.com
Fri Dec 4 13:57:40 CET 2009


Yes, RF in the couple scheme is correct.
The "manual" calculation you did is incorrect.
In the decoupled state the intra-molecular interactions of the decoupled
molecule should not be RF, but plain Coulomb.
The couple option does this correctly.


> Date: Fri, 4 Dec 2009 15:52:58 +0300
> From: ale.odinokov at gmail.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] RF and TI
> Dear gmx users,
> I calculated the hydration free energy of benzene molecule two times.
> First time I used a decoupling method implemented in GROMACS. Second
> time I performed thermodynamical integration between different
> topologies of the benzene molecule: non-interacting with media and
> normal one. All intramolecular interactions were turned off. The
> results were different: decoupling method gave energies about 2.8
> kcal/mol higher. I investigated the problem and found that the
> difference of the <dH/dl> values was due to the Reaction-field term.
> When I switched electrostatic to the simple cut-off scheme, decoupling
> method gave almost the same result, while for dual topology method the
> result increased on 2-3 kcal/mol.
> Is the RF method consistent with free energy calculations? Can it be
> treated within the frames of decoupling scheme?
> Thanks,
> Alexey
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