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Question about w_bins & progress coordinate values

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Nell Karpinski

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Mar 12, 2024, 11:27:34 AM3/12/24
to westpa-users
Hello WESTPA users,

I'm currently working on running a binding simulation of a ligand binding to DNA. As I was checking my h5 file and looking at my progress coordinates, I noticed they do not match up to what is being reflected after I run the w_bins command. 


w_bins -W westBackup.h5 info --detail

Bin information for iteration 57

1048 segments

652 bins total, 0 targets, 131 (20.092%) occupied

Minimum probability by bin:     7.95625748251158061e-25

Maximum probability by bin:     7.38126402997491271e-02

Dynamic range (by bin):         52.8844 kT

Minimum probability by segment: 9.94532185313947576e-26

Maximum probability by segment: 1.43622782517575306e-02

Dynamic range (by segment):     53.327 kT

Norm = 1, error in norm = 0 (0 epsilon)


 Index     Count    Total weight               Min seg weight             Max seg weight             Weight ratio    Label

     0         0    0.00000000000000000e+00    0.00000000000000000e+00    0.00000000000000000e+00         0.00000    [(0.0, 5), (0.0, 1.0), (1.0, 1.5)]

     1         0    0.00000000000000000e+00    0.00000000000000000e+00    0.00000000000000000e+00         0.00000    [(0.0, 5), (0.0, 1.0), (1.5, 1.6)]

     2         0    0.00000000000000000e+00    0.00000000000000000e+00    0.00000000000000000e+00         0.00000    [(0.0, 5), (0.0, 1.0), (1.6, 1.7)]

     3         0    0.00000000000000000e+00    0.00000000000000000e+00    0.00000000000000000e+00         0.00000    [(0.0, 5), (0.0, 1.0), (1.7, 1.8)]

     4         0    0.00000000000000000e+00    0.00000000000000000e+00    0.00000000000000000e+00         0.00000    [(0.0, 5), (0.0, 1.0), (1.8, 1.9)]

     5         0    0.00000000000000000e+00    0.00000000000000000e+00    0.00000000000000000e+00         0.00000    [(0.0, 5), (0.0, 1.0), (1.9, 2.0)]

     6         0    0.00000000000000000e+00    0.00000000000000000e+00    0.00000000000000000e+00         0.00000    [(0.0, 5), (0.0, 1.0), (2.0, 2.1)]

     7         0    0.00000000000000000e+00    0.00000000000000000e+00    0.00000000000000000e+00         0.00000    [(0.0, 5), (0.0, 1.0), (2.1, 2.2)]

     8         0    0.00000000000000000e+00    0.00000000000000000e+00    0.00000000000000000e+00         0.00000    [(0.0, 5), (0.0, 1.0), (2.2, 2.3)]

     9         0    0.00000000000000000e+00    0.00000000000000000e+00    0.00000000000000000e+00         0.00000    [(0.0, 5), (0.0, 1.0), (2.3, 2.4)]

    10         0    0.00000000000000000e+00    0.00000000000000000e+00    0.00000000000000000e+00         0.00000    [(0.0, 5), (0.0, 1.0), (2.4, 2.6)]

    11         0    0.00000000000000000e+00    0.00000000000000000e+00    0.00000000000000000e+00         0.00000    [(0.0, 5), (0.0, 1.0), (2.6, 2.7)]

    12         0    0.00000000000000000e+00    0.00000000000000000e+00    0.00000000000000000e+00         0.00000    [(0.0, 5), (0.0, 1.0), (2.7, 2.8)]

    13         0    0.00000000000000000e+00    0.00000000000000000e+00    0.00000000000000000e+00         0.00000    [(0.0, 5), (0.0, 1.0), (2.8, 3.0)]

    14         0    0.00000000000000000e+00    0.00000000000000000e+00    0.00000000000000000e+00         0.00000    [(0.0, 5), (0.0, 1.0), (3.0, 3.1)]

    15         0    0.00000000000000000e+00    0.00000000000000000e+00    0.00000000000000000e+00         0.00000    [(0.0, 5), (0.0, 1.0), (3.1, 3.2)]

    16         0    0.00000000000000000e+00    0.00000000000000000e+00    0.00000000000000000e+00         0.00000    [(0.0, 5), (0.0, 1.0), (3.2, 3.3)]

    17         0    0.00000000000000000e+00    0.00000000000000000e+00    0.00000000000000000e+00         0.00000    [(0.0, 5), (0.0, 1.0), (3.3, 3.4)]

    18         0    0.00000000000000000e+00    0.00000000000000000e+00    0.00000000000000000e+00         0.00000    [(0.0, 5), (0.0, 1.0), (3.4, 3.5)]

    19         0    0.00000000000000000e+00    0.00000000000000000e+00    0.00000000000000000e+00         0.00000    [(0.0, 5), (0.0, 1.0), (3.5, 3.6)]

    20         0    0.00000000000000000e+00    0.00000000000000000e+00    0.00000000000000000e+00         0.00000    [(0.0, 5), (0.0, 1.0), (3.6, 3.7)]

    21         0    0.00000000000000000e+00    0.00000000000000000e+00    0.00000000000000000e+00         0.00000    [(0.0, 5), (0.0, 1.0), (3.7, 3.8)]

    22         8    1.71117859694508388e-07    1.95912763692248234e-08    3.39789251099346281e-08         1.73439    [(0.0, 5), (0.0, 1.0), (3.8, 3.9)]

    23         8    3.45526947386881015e-07    3.02050282394342050e-08    8.49706208895261268e-08         2.81313    [(0.0, 5), (0.0, 1.0), (3.9, 4.0)]

    24         8    3.13897332079681546e-06    2.96394098150825875e-07    5.92788196301651749e-07         2.00000    [(0.0, 5), (0.0, 1.0), (4.0, 4.1)]

    25         8    5.26037390121114980e-06    5.72970877196522635e-07    1.18557639260330350e-06         2.06917    [(0.0, 5), (0.0, 1.0), (4.1, 4.2)]

    26         8    5.09114681035756711e-05    2.37115278520660700e-06    9.29304797972116754e-06         3.91921    [(0.0, 5), (0.0, 1.0), (4.2, 4.3)]

    27         8    3.01725122700723309e-04    3.03670969335285790e-05    5.22328106665947360e-05         1.72005    [(0.0, 5), (0.0, 1.0), (4.3, 4.4)]

    28         8    1.32566398305301154e-04    1.25266032794830995e-05    2.61164053332973680e-05         2.08488    [(0.0, 5), (0.0, 1.0), (4.4, 4.5)]

    29         8    8.06998705235269015e-04    8.16380764391134279e-05    1.47415432989594290e-04         1.80572    [(0.0, 5), (0.0, 1.0), (4.5, 4.6)]

    30         8    5.76229716112604587e-04    5.01064131179323980e-05    1.06394686986159960e-04         2.12337    [(0.0, 5), (0.0, 1.0), (4.6, 4.7)]

So, for example, it says I have weight in bin index 22:     "22         8    1.71117859694508388e-07    1.95912763692248234e-08    3.39789251099346281e-08         1.73439    [(0.0, 5), (0.0, 1.0), (3.8, 3.9)]", however though, I have 1048 segments in iteration 57, I don't seem to have a segment whose progress coordinates reflect this bin occupancy. If there is anyone that can help with this issue or clarifying something I am missing, I would greatly appreciate the help! Thank you!

Best,
Nell 

gma57

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Mar 12, 2024, 1:05:22 PM3/12/24
to westpa-users
Hi Nell,

Thank you for your question!

The w_bins command reports bin occupancy at the first frame of an iteration. If you check segment locations at any other point in the iteration, they may have changed bins which would cause discrepancies between the occupancy reported by w_bin and the current segment coordinates.

Please feel free to follow up with further questions!

Best,
Gessica Adornato
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