Hi,
the key
Umb. Pos. 0.0
indicates the the umbrella center of this simulaiton is at 0.0, not that
the profile should starts at zero. Beginning and end of profile are set
with -min -max.
cheers,
Jochen
Am 3/22/12 7:03 PM, schrieb rainy908:
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
--
---------------------------------------------------
Dr. Jochen Hub
Computational Molecular Biophysics Group
Institute for Microbiology and Genetics
Georg-August-University of Göttingen
Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
Phone: +49-551-39-14189
http://cmb.bio.uni-goettingen.de/
---------------------------------------------------
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