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@@ -38,6 +38,56 @@ Usage
wham has a convenient command line interface. You can see all options with
```wham -h```:
```
wham 0.9.9
D. Bauer <bauer@bio.tu-darmstadt.de>
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.
USAGE:
wham [FLAGS] [OPTIONS] --bins <BINS> --max <HIST_MAX> --file <METADATA> --min <HIST_MIN> --temperature <temperature>
FLAGS:
-c, --cyclic 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.
-h, --help Prints help information
-V, --version Prints version information
-v, --verbose Enables verbose output.
OPTIONS:
-b, --bins <BINS> Number of histogram bins (comma separated).
--bt <bootstrap> Number of bayesian bootstrapping runs for error analysis by assigning random
weights (defaults to 0).
--seed <bootstrap_seed> Random seed for bootstrapping runs.
--end <end> Skip rows in timeseries with an index larger than this value (defaults to 1e+20)
-i, --iterations <ITERATIONS> Stop WHAM after this many iterations without convergence (defaults to 100,000).
--max <HIST_MAX> Histogram maxima (comma separated). Also accepts "pi".
-f, --file <METADATA> Path to the metadata file.
--min <HIST_MIN> Histogram minima (comma separated for multiple dimensions). Also accepts "pi".
-o, --output <output> Free energy output file (defaults to wham.out).
--start <start> Skip rows in timeseries with an index smaller than this value (defaults to 0)
-T, --temperature <temperature> WHAM temperature in Kelvin.
-t, --tolerance <TOLERANCE> Abortion criteria for WHAM calculation. WHAM stops if abs(F_new - F_old) <
tolerance (defaults to 0.000001).
```
To run the two dimensional example (simulation of dialanine phi and psi angle):
```bash
wham --max 3.14,3.14 --min -3.14,-3.14 -T 300 --bins 100,100 --cyclic -f example/2d/metadata.dat