Dear Chris In relation to the correspondence below, I should've mentioned that the peaks are symmetrical about the equilibrium distance as supposed to the there being one main peak at the equilibrium distance. Also should there be much of difference if you set pull_init to equal the distance between the COMs from the initial configuration, or if you set the value in the mdp file (which may be slightly different from that of the initial configuration). When I set pull_init to equal the that of the initial configuration i.e.pull_init =0 and pull_start = yes, there is much less fluctuation about the equilibrium distance than if I set pull_init to a value that is close to that of the initial configuration. (note all other parameters are the same)
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
