diff --git a/README.md b/README.md index 5e0acbe..316bee3 100644 --- a/README.md +++ b/README.md @@ -12,6 +12,43 @@ Features - Multidimensional - Unit tested +Usage +--- +wham has a convenient command line interface. You can see all options with +```wham -h```: + +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 +> Supplied WHAM options: Metadata=example/2d/metadata.dat, hist_min=[-3.14, -3.14], hist_max=[3.14, 3.14], bins=[100, 100] verbose=false, tolerance=0.000001, iterations=100000, temperature=300, cyclic=true +> Reading input files. +> 625 windows, 624262 datapoints +> Iteration 10: dF=0.389367172324539 +> Iteration 20: dF=0.21450559607810152 +(...) +> Iteration 620: dF=0.0000005800554892309461 +> Iteration 630: dF=0.00000047424278621817084 +> Finished. Dumping final PMF +(... pmf dump ...) + +``` +After convergence, final bias offsets (F) and the free energy will be dumped to stdout and the output file is written. + + +The output file contains the free energy and probability for each bin. Probabilities are normalized to sum to P=1.0 and +the smallest free energy is set to 0 (with other free energies based on that). +``` +#coord1 coord2 Free Energy Probability +-3.109590 -3.109590 10.330312 0.000095 +-3.046770 -3.109590 8.907360 0.000168 +-2.983950 -3.109590 7.431969 0.000303 +-2.921130 -3.109590 6.170882 0.000502 +-2.858310 -3.109590 4.982956 0.000809 +-2.795490 -3.109590 3.584741 0.001417 +-2.732670 -3.109590 3.025337 0.001773 +(...) +``` + Examples --- The example folder contains input and output files for two simple test systems: