Dear GMX community I am trying to perform free energy calculation and encounter a problem similar to that in the discusion in September (theme "Free Energy of Binding Question") This problem arises both in the complex with protein and with the ligand in water. It appears in the step where ligand starts to recouple (I start from the decoupled ligand and consequently turn on vdw and then charges). And the dG between the zero and the first init_lambda appears about 1800 kJ/mol ( This problem remains if we use npt.xvg files for BAR instead of md). All other dG are not higher than 10 kJ/mol and all negative. But the first one is too high and positive.
Here are parameters concerning free energy calculations. free_energy=yes couple-moltype = UNK couple-intramol = no couple-lambda0 = none couple-lambda1 = vdw-q init_lambda_state = 0 calc_lambda_neighbors = 1 vdw_lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 nstdhdl = 100 Also please find attached energy minimization, nvt and npt mdp files and files from the BAR analysis: http://turbobit.net/6ow5sa65wn6x.html This problem remains when switching between Gromacs2016 and Gromacs 5.1.4. Sincerely yours, Vladislav Balaev -- 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.
