O.K thanks anyway
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
