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Analyzing and biasing simulations with PLUMED
Giovanni Bussi, Gareth A. Tribello
This chapter discusses how the PLUMED plugin for molecular dynamics can be used to analyze and bias molecular dynamics trajectories. The chapter begins by introducing the notion of…
The mechanism of RNA base fraying: molecular dynamics simulations analyzed with core-set Markov state models
Giovanni Pinamonti, Fabian Paul, Frank Noé +2
The process of RNA base fraying (i.e. the transient opening of the termini of a helix) is involved in many aspects of RNA dynamics. We here use molecular dynamics simulations and M…
Using the Maximum Entropy Principle to Combine Simulations and Solution Experiments
Andrea Cesari, Sabine Reißer, Giovanni Bussi
Molecular dynamics (MD) simulations allow investigating the structural dynamics of biomolecular systems with unrivaled time and space resolution. However, in order to compensate fo…