Hi Justin I am not using periodic boundary conditions for the simulations. I may have sorted it out now. I was generating velocities in the umbrella.mdp file, I have since set gen_vel = no, and the histogram has the correct shape (should this make a difference?)
Cheers Gavin Justin A. Lemkul wrote: > > Have you watched the trajectory? That will show you what your pull > group is doing. Is this a periodicity effect? It should be fairly > obvious iff the sign of dX, etc flip-flops in the pullx.xvg file. > > -Justin > > Gavin Melaugh wrote: >> Thanks Chris and Justin >> >> I do get the output I want from grompp(below). The distance of 5.507 nm >> is the distance that I want to start with and I assume it is therefore >> the equilibrium distance for the harmonic potential. The COM distances >> from the simulations fluctuate around this value which is what I want, >> although my histogram is the wrong shape. >> >> Pull group natoms pbc atom distance at start reference at t=0 >> 0 84 42 >> 1 84 126 >> 5.507 5.507 >> >> Cheers >> >> Gavin >> >> chris.ne...@utoronto.ca wrote: >>> I missed that pull_start = yes, sorry. So Gavin, your run should have >>> stayed around the starting position. Make the histogram directly and >>> you should get a better idea. >>> >>> Chris. >>> >>> -- original message -- >>> >>> >>> To clarify, the tutorial sets "pull_init1 = 0" because it is used in >>> conjunction >>> with "pull_start = yes," in order to take the starting COM distance as >>> the >>> reference. Check the grompp output to verify that you're getting what >>> you think >>> you should be. Otherwise, you'd have to set "pull_start = no" and >>> modify your >>> .mdp file to reflect the proper value of pull_init1 for every window. >>> >>> -Justin >>> >>> >>> >>> >> > -- 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
