refractoring

README.md

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+# Python module for adaptive umbrella sampling
+
+This module can be used to perform adaptive umbrella sampling of a multi-dimensional potential of mean force. The
+algorithm involves::
+
+1) calculate the free energy landscape
+2) Among existing windows, select windows with E < E_max
+3) For each selected window, generate 3^N-1 neighbor windows
+4) Sample new windows, then go to 1) or stop if no new windows can be found
+
+For more details about the algorithm: See
+
+Self-Learning Adaptive Umbrella Sampling Method for the Determination of Free Energy Landscapes in Multiple Dimensions (Wojtas-Niziurski†, Meng, Roux, Bernèche, 2013)
+[(https://doi.org/10.1021/ct300978b)](https://doi.org/10.1021/ct300978b)
+