I think using Perturbation method is more appropriate for this kind of free energy calculation. Check Leach, Molecular Modelling Principle and Applications pp 554-568. Its clearly described there and you can implement it in GROMACS.
Cheers, Emanuel ========================================================= Emanuel Birru PhD Candidate Faculty of Pharmacy and Pharmaceutical Sciences Monash University (Parkville Campus) 381 Royal Parade, Parkville Victoria 3052, Australia Tel: Int + 61 3 9903 9187 E-mail: emanuel.bi...@monash.edu www.pharm.monash.edu.au -----Original Message----- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Fabian Casteblanco Sent: Tuesday, 4 October 2011 6:28 AM To: gmx-users@gromacs.org Subject: [gmx-users] Free Energy Question Hello all, I have a general question about calculating free energies. I recently used g_bar to calculate the free energies of decoupling coulombic and vdW forces of a solute molecule in solvent. I now need to calculate the free energy of a solute molecule mutating to a new molecule (identical but with an extra -CH3 group) in a vacuum and in a solvent. Does anybody know if it would be better to use g_Bar again but this time having the extra -CH3 group completely decoupled by itself or with it be better to use the older slow-growth method that the Gromacs Manual talks about in Sec 3.12. I'm not sure if there is a way to only decouple a certain part of a molecule using the g_bar method, rather than decoupling the entire molecule. Thanks for your help. -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering PhD Student C: +908 917 0723 E: fabian.castebla...@gmail.com -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
