[gmx-users] RF and TI
ale.odinokov at gmail.com
Sat Dec 5 15:38:40 CET 2009
But my system is rigid benzene molecule, and all intramolecular
interactions are absent.
The RF modifies a short-range electrostatic potential. Is it correct
for both decoupling scheme and "manual" method? Where is the
difference? And what about additive constant (named Crf in the manual,
formula 4.14), is it also included in the <dH/dl>?
2009/12/4 Berk Hess <gmx3 at hotmail.com>:
> 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?
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