diff --git a/README.md b/README.md index ff63071..6553ccd 100644 --- a/README.md +++ b/README.md @@ -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 +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 --max --file --min --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 Number of histogram bins (comma separated). + --bt Number of bayesian bootstrapping runs for error analysis by assigning random + weights (defaults to 0). + --seed Random seed for bootstrapping runs. + --end Skip rows in timeseries with an index larger than this value (defaults to 1e+20) + -i, --iterations Stop WHAM after this many iterations without convergence (defaults to 100,000). + --max Histogram maxima (comma separated). Also accepts "pi". + -f, --file Path to the metadata file. + --min Histogram minima (comma separated for multiple dimensions). Also accepts "pi". + -o, --output Free energy output file (defaults to wham.out). + --start Skip rows in timeseries with an index smaller than this value (defaults to 0) + -T, --temperature WHAM temperature in Kelvin. + -t, --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