Hello, I am willing to study the free energy of binding of a cation (Ca++) to the protein and I am following the free energy tutorial provided by Justin (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy ). Please let me know whether the settings for this type of study would be same as given in the tutorial for ligand-Protein binding free energy calculation or it need some different approach: The setting from the ligand-Protein binding free energy calculation are given as:
van der Waals coupling: sc-alpha = 0.5 ; use soft-core for LJ (de)coupling sc-sigma = 0.3 sc-power = 1 couple-moltype = LIG couple-intramol = no couple-lambda0 = none ; non-interacting dummy in state A couple-lambda1 = vdw ; only vdW terms on in state B Coulombic coupling: sc-alpha = 0 ; soft-core during (dis)charging can be unstable! sc-sigma = 0 couple-moltype = LIG couple-intramol = no couple-lambda0 = vdw ; only vdW terms in state A (the previous state B is now A) couple-lambda1 = vdw-q ; all nonbonded interactions are on in state B -- ----------------------- Regards, Bipin Singh -- 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