Hi all, I am experiencing a potential problem with my PMF curve not starting at position 0 of the reaction coordinate, which is defined by a path starting from 0.0 nm and ending at 0.5 nm. When I run the GROMACS g_wham analysis at Umb. Pos 0.0 (see below), to say, 0.02 nm, the PMF curve doesn't start out at 0.0 nm but gets offset to ~0.01 nm in the resulting figure. Its corresponding histogram also gets offset by the same amount. This is particularly peculiar to me because my frame1 *is* the structure at 0.0nm of the S path. I also double-checked my COLVAR file and there are no negative values in my COLVAR file:
# UMBRELLA 3.0 # Compnent selection: 0 0 1 # nSkip 1 # Ref. Group 'TestAtom' # Nr. of pull groups 1 # Group 1 'GR1' Umb. Pos. 0.0 Umb. Cons. 50000 ##### 0.0300 0.000047500 0.0400 0.000103337 0.0500 0.000163820 0.0600 0.000265547 0.0700 0.000408777 0.0800 0.000550200 0.0900 0.000653522 Has anyone else experienced this problem before? I'm hoping it's just some minor issue in g_wham. I even invoked the -zprof0 flag to "- zprof 0" and it did not set my PMF curve to start at 0. Sincerely, Lili -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
