Re: [gmx-users] RF and TI
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? Alexey 2009/12/4 Berk Hess g...@hotmail.com: Hi, 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. Berk Date: Fri, 4 Dec 2009 15:52:58 +0300 From: ale.odino...@gmail.com To: gmx-users@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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php New Windows 7: Find the right PC for you. Learn more. -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] RF and TI
Hi, 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. Berk Date: Fri, 4 Dec 2009 15:52:58 +0300 From: ale.odino...@gmail.com To: gmx-users@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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ New Windows 7: Find the right PC for you. Learn more. http://windows.microsoft.com/shop-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
