Dear Chris Thanks but I am not using periodic boundary conditions as I want to simulate the two molecules in a vacuum.
Gavin chris.ne...@utoronto.ca wrote: > Dear Gavin: > > plot the position vs. time. Probably you will see it sample around one > value, then discover a new state, and make a sharp transition to > another value. If the new state is much more favourable than the > initial state, then you can discard the initial state as > equilibration. It might not be though... > > Also, could you have a PBC problem? I suggest that you read up on > pull_pbcmol and try some tests with smart values of pull_pbcmol. > > Chris. > > -- original message -- > > 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
