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 ? Alexey 2009/12/4 Berk Hess : > 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 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 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
[gmx-users] density and intramolecular interactions
Hi everyone, I have a model for liquid benzene. In this model all bonds are treated as harmonic potentials. When I use larger constants for these potentials (to make molecules more planar), the average density of my benzene (from NPT ensemble) becomes lower. Does virial depend on intramolecular interactions? If a want to make benzene molecules completely rigid (through the virtual sites, for example), can I use the same parameters for intermolecular interactions? Thank you in advance, 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
[gmx-users] Re: RE: question about PME
We wish to withdraw the direct interaction between the ions and learn how it appears in the computed PMF profile. As a true Coulomb value? Or as its Ewald counterpart contaminated by periodic effects? In the latter case we are looking for the pertaining correction. Is it available? Or is it unneccesary? -- Message: 5 Date: Fri, 4 Sep 2009 12:47:05 +0200 From: Berk Hess Subject: RE: [gmx-users] question about PME To: Discussion list for GROMACS users Message-ID: Content-Type: text/plain; charset="iso-8859-1" This is tricky matter. The direct interaction between the ions is 1/(4 pi eps0) r (ignoring periodic effects). However, the interaction is screened by the water and therefore the effective interaction is 1/(4 pi eps0 epsr) r, where epsr is the dielectric constant of the water model. The periodic effects depend on the distance relative to the box size and they depend on the complete contents of the system. I don't understand what you want to determine exactly. Berk Date: Fri, 4 Sep 2009 14:36:30 +0400 From: ale.odino...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] question about PME Hello everyone, We calculate the potential of mean force (PMF) for the ion pair AB (the solute) in a solvent. The computation is made in terms of the COM pulling. The PMF includes both the solute-solvent and intrasolute interactions. We are interested only in the solvation energy, i. e. the electroststic interaction between A and B must be eliminated from the PMF. The question is, whether we have to subtract the true Coulomb energy 1/R (R is the inter-ionic distance) or this term is distorted during the PME computation and must be modified in some way before being subtracted. Thanks in advance for your help,Alexey Odinokov ___ 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] question about PME
Hello everyone, We calculate the potential of mean force (PMF) for the ion pair AB (the solute) in a solvent. The computation is made in terms of the COM pulling. The PMF includes both the solute-solvent and intrasolute interactions. We are interested only in the solvation energy, i. e. the electroststic interaction between A and B must be eliminated from the PMF. The question is, whether we have to subtract the true Coulomb energy 1/R (R is the inter-ionic distance) or this term is distorted during the PME computation and must be modified in some way before being subtracted. Thanks in advance for your help, Alexey Odinokov ___ 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
