159 citations · 457 across the 18 of their papers we have counts for
5 papers · 1 filter
PLUMED Tutorials: a collaborative, community-driven learning ecosystem
Gareth A. Tribello, Massimiliano Bonomi, Giovanni Bussi +60
In computational physics, chemistry, and biology, the implementation of new techniques in a shared and open source software lowers barriers to entry and promotes rapid scientific p…
Advanced simulations with PLUMED: OPES and Machine Learning Collective Variables
Enrico Trizio, Andrea Rizzi, Pablo M. Piaggi +2
Many biological processes occur on time scales longer than those accessible to molecular dynamics simulations. Identifying collective variables (CVs) and introducing an external po…
Descriptors-free Collective Variables From Geometric Graph Neural Networks
Jintu Zhang, Luigi Bonati, Enrico Trizio +4
Enhanced sampling simulations make the computational study of rare events feasible. A large family of such methods crucially depends on the definition of some collective variables…
Combining transition path sampling with data-driven collective variables through a reactivity-biased shooting algorithm
Jintu Zhang, Odin Zhang, Luigi Bonati +1
Rare event sampling is a central problem in modern computational chemistry research. Among the existing methods, transition path sampling (TPS) can generate unbiased representation…
Deep learning path-like collective variable for enhanced sampling molecular dynamics
Thorben Fröhlking, Luigi Bonati, Valerio Rizzi +1
Several enhanced sampling techniques rely on the definition of collective variables to effectively explore free energy landscapes. Existing variables that describe the progression…