[gmx-users] g_wham position 0

rainy908 rainy908 at yahoo.com
Thu Mar 22 19:03:47 CET 2012

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.


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