Statistical Biophysics Blog

Molecular dynamics simulations often fail to reach timescales characteristic of equilibrium sampling, so great care must be taken in computing and reporting statistical u [...]

The potential of mean force (PMF) is one of the most widely used characterizations of a biomolecular system computed from simulation, but calculating and interpreting a P [...]

Terrell Hill's book, Free Energy Transduction and Biochemical Cycle Kinetics, is one of the most important introductory-level contributions to the biophysics of molecular [...]

A concise overview of the weighted ensemble path sampling method for rare events is given, aimed at beginners.

Basic concepts and limitations of path sampling are described.

The basics of trajectories and the different types of trajectory ensembles are explained.

The trajectory ensemble is fundamental in statistical physics and relatively easy to understand. It is also information-rich, as both equilibrium and non-equilibrium obse [...]

Most behavior, observed via a subset of coordinates or discretized states, should not be Markovian even though the underlying dynamics generally will be.

The "Hill relation" is a key result for anyone interested in calculating rates from trajectories of any kind, whether molecular simulations or otherwise. I am not aware o [...]