Spline String Method

Overview

pysages.methods.spline_string.SplineString(...)

This class combines UmbrellaIntegration of multiple replicas with the path evolution of the spline (improved) string method.

Details

Spline String method (aka Improved String method). The improved string methods finds the local minimum free-energy path (MFEP) trough a given landscape. It uses umbrella integration to advance the discretized replicas in the CV space. A spline interpolation helps to (equally) space the CV points along the string. The process converges if the MFEP is found. The final free-energy profile is calculated the same way as in UmbrellaIntegration. We aim to implement this: Weinan, E., et. al. J. Chem. Phys. 126.16 (2007): 164103.

class pysages.methods.spline_string.SplineString(cvs, ksprings, centers, alpha, hist_periods: ~typing.List | int, hist_offsets: ~typing.List | int = 0, metric: ~typing.Callable = <function SplineString.<lambda>>, spacing: ~typing.List | None = None, freeze_idx: ~typing.List = [], **kwargs)

This class combines UmbrellaIntegration of multiple replicas with the path evolution of the spline (improved) string method. 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.