Hi! Dear gmx users, I have md simmulations of a protein with four different ligands. now I want to calculate the free energy of binding. which method does suit after md simmulation? either g_mmpbsa or gmx BAR method. If I use BAR method is it necessary to set charges to zero as in the tutorial given at http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/03_workflow.html.
I s necessary to turn off couloumb interactions for calculating free energy of ligand protein complex. if i want to use coloumb interactions also then should i set the coul_lambdas values in the same way as vdw_lambdas. Another question is that there is another tutorial available at http://www.gromacs.org/@api/deki/files/262/=gromacs-free-energy-tutorial.pdf In this tutorial the system has been equilliberated before generating the lambda states. while in the justin tutorial each lambda state is equiliberated separately. kindly tell me which one is more suitable for a protein ligand complex. looking forward for your cooperation. sorry if the questions are trivial. Regards Neelam Ph.D scholar -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
