Hi all I am generating a potential of mean force curve for the interaction between two cage molecules using umbrella sampling. The system is composed of only the two molecules in question, using no pbc and no cut-offs. Umbrella sampling is performed at 25 different distances (between COMs) between 0.75 and 2.75 nm. The histogram generated form g_wham shows very good overlap between the histogram between 0.75 nm and 2 nm. The shapes of the histogram and the width of the distribution are all well in this region. Above 2nm the histograms show two peaks and therefore the shape and distribution at these distances is poor. Has anyone ever come across this sort of behaviour before? Also can you use different force constants for the harmonic potential at different distances ?
Cheers Gavin p.s Here is a copy of the mdp file that I am using title = Pull test cpp = include = define = integrator = md nsteps = 50000000 dt = 0.002 nstxout = 250000 nstvout = 250000 nstlog = 250000 nstenergy = 5000 nstfout = 250000 pbc = no nstlist = 10 ns_type = simple vdwtype = cut-off rlist = 0 rvdw_switch = 0 rvdw = 0 coulombtype = cut-off rcoulomb = 0 tcoupl = nose-hoover tc_grps = system tau_t = 0.1 ref_t = 600 gen_vel = no gen_temp = constraints = none comm_mode = angular pull = umbrella pull_geometry = distance pull_dim = Y Y Y pull_start = no pull_ngroups = 1 pull_group0 = cage_1 pull_group1 = cage_2 pull_init1 = 2.59 pull_rate1 = 0.0 pull_k1 = 1000 pull_nstxout = 1000 pull_nstfout = 1000 -- 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/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/mailing_lists/users.php
