pysages.methods.umbrella_integration

Overview

pysages.methods.umbrella_integration.UmbrellaIntegration(...)

This class combines harmonic biasing with multiple replicas.

Details

Umbrella Integration.

Umbrella integration uses multiple replicas placed along a pathway in the free energy landscape by Harmonic Bias simulations. From the statistics of the simulations, the thermodynamic forces along the path are determined and integrated to obtain an approximation of the free energy landscape. This class implements the replica simulations and approximates the free energy. However, the method is not very accurate and it is preferred that more advanced methods (e.g. the Weighted Histogram Analysis Method) are used for the analysis of the simulations.

class pysages.methods.umbrella_integration.UmbrellaIntegration(cvs, ksprings, centers, hist_periods: list | int, hist_offsets: list | int = 0, **kwargs)

This class combines harmonic biasing with multiple replicas. It also collects histograms of the collective variables throughout the simulations for subsequent analysis. By default the class also estimates an approximation of the free energy landscape along the given path via umbrella integration. Note that this is not very accurate and usually requires more sophisticated analysis on top.