I always used g_dist to plot the COM distances because the pullx.xvg files doesn't give this value directly. Can you access the COM distance from the pullx.xvg file
Gavin Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> Justin >> >> I have looked at the movies but it's very hard to tell what's going on >> as I save teh trajectories every 250000 steps for every 50000000 step >> simulation (100 ns). Ill look at them again in more detail and post >> back. >> > > Plotting the pullx.xvg file(s) may be useful, too, to indicate where > any weird jumps or sudden changes in position might occur. Mapping > that information back onto the trajectory could help focus your > attention. > > -Justin > >> Gavin >> >> Justin A. Lemkul wrote: >>> >>> Gavin Melaugh wrote: >>>> O.K thanks anyway >>>> >>> I saw the plots you posted during a conversation with Chris, but I'll >>> ask the obvious anyway: have you watched the trajectories for any of >>> the problematic windows? It didn't seem like you had two metastable >>> states, but maybe having a look at the movie would shed some light on >>> what's going on. I know that's the first thing I'd do. >>> >>> -Justin >>> >>>> Justin A. Lemkul wrote: >>>>> Gavin Melaugh wrote: >>>>>> Thanks Justin >>>>>> >>>>>> Have you any idea why when generating umbrella histograms for the >>>>>> pmf I >>>>>> would get two peaks in the histograms above a distance of 2 nm, but >>>>>> below 2 nm I get well behaved histograms that lead to a very >>>>>> good profile in the pmf. To the best of my knowledge the >>>>>> configurations >>>>>> are all very well equilibrated at their respective COM distances. >>>>>> Umbrella sampling is performed on all windows using a force >>>>>> constant of >>>>>> 1000 kj/mol at 600 K. >>>>>> >>>>> Sorry, no clue. >>>>> >>>>> -Justin >>>>> >>>>>> Cheers >>>>>> >>>>>> Gavin >>>>>> >>>>>> Justin A. Lemkul wrote: >>>>>>> Justin A. Lemkul wrote: >>>>>>>> Gavin Melaugh wrote: >>>>>>>>> Hi all >>>>>>>>> >>>>>>>>> I am generating a series of configurations using the pull code to >>>>>>>>> calculate the pmf. I am using no pbc i.e. pbc =no, howver the >>>>>>>>> output >>>>>>>>> from grommp gives me info on pbc atom. >>>>>>>>> >>>>>>>>> Pull group natoms pbc atom distance at start reference at >>>>>>>>> t=0 >>>>>>>>> 0 72 36 >>>>>>>>> 1 72 360 4.290 4.290 >>>>>>>>> >>>>>>>>> why is this so? >>>>>>>>> >>>>>>>> grompp always assigns the numerical middle atom of a group as the >>>>>>>> PBC >>>>>>> ...unless over-ridden by providing a different value for >>>>>>> pbc_pullatom1. >>>>>>> >>>>>>> -Justin >>>>>>> >>>>>>>> reference point. In the case of pbc=no, it shouldn't matter. >>>>>>>> >>>>>>>> http://manual.gromacs.org/current/online/mdp_opt.html#pull >>>>>>>> >>>>>>>> -Justin >>>>>>>> >>>>>>>>> Cheers >>>>>>>>> >>>>>>>>> Gavin >>>> >> >> > -- 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
