[gmx-users] g_wham position 0

[Jochen Hub]

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

-- 
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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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