O.K thanks Justine I'll look at these files and see if there is any weirdness. Just to make sure that there are no cut-off artefacts. If I set the cut-offs to zero as in the following mdp file; that does mean that I am considering all electrostatic and LJ interactions between the molecules? and not including them at all. I assume the former given that there are both electrostatic and LJ energy values in the log and energy files.
Gavin 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 Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> For the umbrella sampling I am not pulling in any direction I am just >> applying the umbrella potential so that two molecules can sample space >> about a give value of r0 (COM distance). Maybe I am confused but should >> I not plot the absolute value of the displacement (modulus) as supposed >> to the displacement along a given vector component? >> > > For diagnosing weird behavior, I would always start with the primary > data, not any post-processed interpretation of it. Use the pullx.xvg > file. Any weird changes in sign or sudden changes in magnitude would > indicate problems. If you start manipulating the data, you may be > hiding the real reason for the problem. > > -Justin > >> Gavin >> >> Justin A. Lemkul wrote: >>> >>> Gavin Melaugh wrote: >>>> 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 >>>> >>> That's what is in pullx.xvg - coordinate (X,Y,Z) of the reference >>> group, then displacement (dX,dY,dZ) of the pull group relative to the >>> reference. Not all terms may be present, depending on the axis along >>> which you're pulling, i.e. if you only pull along Z, there will be two >>> terms in pullx.xvg - Z and dZ. >>> >>> -Justin >>> >>>> 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 [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
