Hi, I'm preparing my mdp and topology files for running free energy calculations using BAR method. I´m using Justin Lemkul's tutorial as a reference (You can find it here http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/08_advanced.html). According to this tutorial, the simultaneous coupling of both Coulombic and van der Waals terms leads to instability. So, it is usefull to prepare the mdp files as follows (off course including all other parameters):
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 However, I don't understand how can this leads to a fully interacting molecule if all the charges in the topology file have been set to zero. Does it mean that for the second calculation (coulombic coupling) I have to use the original topology file with all charges? Or, should I use the same topology with zero charges? Thanks in advance, Sonia Aguilera Graduate student-Chemical Engineering Department Universidad de los Andes Colombia -- 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