PyRETIS 2: An improbability drive for rare events

Predicting the mechanism and rate of H-NS binding to AT-rich DNA

(2019) Enrico Riccardi et al.   PLoS Computational Biology

Envisioning data sharing for the biocomputing community

(2019) Enrico Riccardi et al.   Interface Focus

Local initiation conditions for water autoionization

(2018) Mahmoud Moqadam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

OpenPathSampling: A Python Framework for Path Sampling Simulations. 1. Basics

(2018) David W. H. Swenson et al.   Journal of Chemical Theory and Computation

OpenPathSampling: A Python Framework for Path Sampling Simulations. 2. Building and Customizing Path Ensembles and Sample Schemes

(2018) David W. H. Swenson et al.   Journal of Chemical Theory and Computation

PyRETIS: A well-done, medium-sized python library for rare events

(2017) Anders Lervik et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Fast Decorrelating Monte Carlo Moves for Efficient Path Sampling

(2017) Enrico Riccardi et al.   Journal of Physical Chemistry Letters

The atomic simulation environment—a Python library for working with atoms

(2017) Ask Hjorth Larsen et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Rare event simulations reveal subtle key steps in aqueous silicate condensation

(2017) Mahmoud Moqadam et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

(2017) Peter Eastman et al.   PLoS Computational Biology

Analyzing Complex Reaction Mechanisms Using Path Sampling

(2016) Titus S. van Erp et al.   Journal of Chemical Theory and Computation

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

(2015) Robert T. McGibbon et al.   BIOPHYSICAL JOURNAL

cp2k: atomistic simulations of condensed matter systems

(2013) Jürg Hutter et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

(2012) Peter Eastman et al.   Journal of Chemical Theory and Computation

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

(2011) Naveen Michaud-Agrawal et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

(2008) Alessandro Laio et al.   REPORTS ON PROGRESS IN PHYSICS