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Hi,<br><br>Yes, RF in the couple scheme is correct.<br>The "manual" calculation you did is incorrect.<br>In the decoupled state the intra-molecular interactions of the decoupled<br>molecule should not be RF, but plain Coulomb.<br>The couple option does this correctly.<br><br>Berk<br><br>> Date: Fri, 4 Dec 2009 15:52:58 +0300<br>> From: ale.odinokov@gmail.com<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] RF and TI<br>> <br>> Dear gmx users,<br>> I calculated the hydration free energy of benzene molecule two times.<br>> First time I used a decoupling method implemented in GROMACS. Second<br>> time I performed thermodynamical integration between different<br>> topologies of the benzene molecule: non-interacting with media and<br>> normal one. All intramolecular interactions were turned off. The<br>> results were different: decoupling method gave energies about 2.8<br>> kcal/mol higher. I investigated the problem and found that the<br>> difference of the <dH/dl> values was due to the Reaction-field term.<br>> When I switched electrostatic to the simple cut-off scheme, decoupling<br>> method gave almost the same result, while for dual topology method the<br>> result increased on 2-3 kcal/mol.<br>> Is the RF method consistent with free energy calculations? Can it be<br>> treated within the frames of decoupling scheme?<br>> <br>> Thanks,<br>> <br>> Alexey<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>                                            <br /><hr />New Windows 7: Find the right PC for you. <a href='http://windows.microsoft.com/shop' target='_new'>Learn more.</a></body>
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