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89 lines
3.1 KiB
YAML
89 lines
3.1 KiB
YAML
name: wham
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version: "0.9.0"
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author: D. Bauer <bauer@bio.tu-darmstadt.de>
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about: |
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wham is a fast implementation of the weighted histogram analysis method (WHAM) written in Rust. It currently supports potential of mean force (PMF) calculations in multiple dimensions at constant temperature.
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Metadata file format:
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/path/to/timeseries_file1 x_1 x_2 x_N fc_1 fc_2 fc_N
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/path/to/timeseries_file2 x_1 x_2 x_N fc_1 fc_2 fc_N
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/path/to/timeseries_file3 x_1 x_2 x_N fc_1 fc_2 fc_N
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The first column is a path to a timeseries file _relative_ to the metadata file (see below). This is followed by the position of the umbrella potential x in N dimensions and the force constant fc in each dimension. Lines starting with a # are treated as comments and will not be parsed.
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Timeseries file format:
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time x_1 x_2 x_N
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time x_1 x_2 x_N
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time x_1 x_2 x_N
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The first column will be ignored and is followed by N reaction coordinates x.
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Shipped under the GPLv3 license.
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args:
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- metadata:
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short: f
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long: file
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value_name: METADATA
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takes_value: true
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required: true
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help: Path to the metadata file.
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- min_hist:
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long: min
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value_name: HIST_MIN
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takes_value: true
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required: true
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allow_hyphen_values: true
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help: Histogram minima (comma separated for multiple dimensions).
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- max_hist:
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long: max
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value_name: HIST_MAX
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takes_value: true
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required: true
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allow_hyphen_values: true
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help: Histogram maxima (comma separated)
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- bins:
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short: b
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long: bins
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value_name: BINS
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takes_value: true
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required: true
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help: Number of histogram bins (comma separated).
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- tolerance:
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short: t
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long: tolerance
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value_name: TOLERANCE
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takes_value: true
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required: false
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help: Abortion criteria for WHAM calculation. WHAM stops if abs(F_new - F_old) < tolerance (defaults to 0.000001).
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- iterations:
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short: i
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long: iterations
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value_name: ITERATIONS
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takes_value: true
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required: false
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help: Stop WHAM after this many iterations without convergence (defaults to 100,000).
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- cyclic:
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short: c
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long: cyclic
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help: For periodic reaction coordinates. If this is set, the first and last coordinate bin in each dimension are treated as neighbors for the bias calculation.
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- verbose:
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short: v
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long: verbose
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help: Enables verbose output.
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takes_value: false
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- temperature:
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short: T
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long: temperature
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help: WHAM temperature in Kelvin.
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takes_value: true
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required: true
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- output:
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short: o
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long: output
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help: Free energy output file (defaults to wham.out).
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takes_value: true
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required: false
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- bootstrap:
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long: bt
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help: Number of bayesian bootstrapping runs for error analysis by assigning random weights (defaults to 0).
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takes_value: true
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required: false
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