String Method

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Introduction

The string method (STM) is an enhanced sampling technique for identifying the most probable transition pathway (minimum free-energy path) between two or more states in high-dimensional collective-variable space. The method discretises the path into a series of connected points (beads) and iteratively refines their positions using biased molecular dynamics to align the path with the underlying free energy landscape.

PMFLib implements the approach described in the article String Method in Collective Variables: Minimum Free Energy Paths and Isocommittor Surfaces [1] with many improvements. The path is described using splines (interpolating or smoothing) and optimised with advanced gradient-based algorithms such as ADM (Adaptive Moment Estimation) and its variants. Technically, the implementation uses a client/server architecture and operates in two modes, synchronous and asynchronous, enabling effective utilisation of various computational resources.

Contents

• STM:Server
  • STM:Server Controls
  • STM:Path
• STM:Client
  • STM:Client Controls
  • STM:Collective variables
• STM:Post-processing
• STM:Utilities
• STM:Examples

References

(1) Maragliano, L.; Fischer, A.; Vanden-Eijnden, E.; Ciccotti, G. String Method in Collective Variables: Minimum Free Energy Paths and Isocommittor Surfaces. J. Chem. Phys. 2006, 125 (2), 024106. https://doi.org/10.1063/1.2212942.