name: wham
version: "1.1.3"
author: D. Bauer <bauer@bio.tu-darmstadt.de>
about: |
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.
Metadata file format:
/path/to/timeseries_file1 x_1 x_2 x_N fc_1 fc_2 fc_N
/path/to/timeseries_file2 x_1 x_2 x_N fc_1 fc_2 fc_N
/path/to/timeseries_file3 x_1 x_2 x_N fc_1 fc_2 fc_N
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.
Timeseries file format:
time x_1 x_2 x_N
time x_1 x_2 x_N
time x_1 x_2 x_N
The first column will be ignored and is followed by N reaction coordinates x.
Shipped under the GPLv3 license.
args:
- metadata:
short: f
long: file
value_name: METADATA
takes_value: true
required: true
help: Path to the metadata file.
- min_hist:
long: min
value_name: HIST_MIN
takes_value: true
required: true
allow_hyphen_values: true
help: Histogram minima (comma separated for multiple dimensions). Also accepts "pi".
- max_hist:
long: max
value_name: HIST_MAX
takes_value: true
required: true
allow_hyphen_values: true
help: Histogram maxima (comma separated). Also accepts "pi".
- bins:
short: b
long: bins
value_name: BINS
takes_value: true
required: true
help: Number of histogram bins (comma separated).
- tolerance:
short: t
long: tolerance
value_name: TOLERANCE
takes_value: true
required: false
help: Abortion criteria for WHAM calculation. WHAM stops if abs(F_new - F_old) < tolerance (defaults to 0.000001).
- iterations:
short: i
long: iterations
value_name: ITERATIONS
takes_value: true
required: false
help: Stop WHAM after this many iterations without convergence (defaults to 100,000).
- cyclic:
short: c
long: cyclic
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.
- verbose:
short: v
long: verbose
help: Enables verbose output.
takes_value: false
- temperature:
short: T
long: temperature
help: WHAM temperature in Kelvin.
takes_value: true
required: true
- output:
short: o
long: output
help: Free energy output file (defaults to wham.out).
takes_value: true
required: false
- bootstrap:
long: bt
help: Number of bayesian bootstrapping runs for error analysis by assigning random weights (defaults to 0).
takes_value: true
required: false
- bootstrap_seed:
long: seed
help: Random seed for bootstrapping runs.
takes_value: true
required: false
- start:
long: start
help: Skip rows in timeseries with an index smaller than this value (defaults to 0)
takes_value: true
required: false
- end:
long: end
help: Skip rows in timeseries with an index larger than this value (defaults to 1e+20)
takes_value: true
required: false
- uncorr:
short: g
long: uncorr
help: Estimates statistical inefficiency of each timeseries via autocorrelation and removes correlated samples (default is off).
takes_value: false
required: false
- convdt:
long: convdt
help: "Performs WHAM for slices with the given delta in time and returns an output file for each slice. THis is useful to check the result for convergence. Example: with --convdt 100 and a timeseries ranging from 0-300, free energy surfaces for slices 0-100, 0-200 and 0-300 will be given returned."
takes_value: true
required: false
- ignore_empty:
long: ignore_empty
help: If this is set, do not fail if a histogram is empty.
takes_value: false
required: false