Promoting transparency and reproducibility in enhanced molecular simulations

ELF: An Extended-Lagrangian Free Energy Calculation Module for Multiple Molecular Dynamics Engines

(2018) Haochuan Chen et al.   Journal of Chemical Information and Modeling

SSAGES: Software Suite for Advanced General Ensemble Simulations

(2018) Hythem Sidky et al.   JOURNAL OF CHEMICAL PHYSICS

Recruiting machine learning methods for molecular simulations of proteins

(2018) Shriyaa Mittal et al.   MOLECULAR SIMULATION

Biophysical experiments and biomolecular simulations: A perfect match?

(2018) Sandro Bottaro et al.   SCIENCE

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

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

Free Energy Reconstruction from Logarithmic Mean-Force Dynamics Using Multiple Nonequilibrium Trajectories

(2017) Tetsuya Morishita et al.   Journal of Chemical Theory and Computation

Navigating at Will on the Water Phase Diagram

(2017) S. Pipolo et al.   PHYSICAL REVIEW LETTERS

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

(2017) Peter Eastman et al.   PLoS Computational Biology

HTMD: High-Throughput Molecular Dynamics for Molecular Discovery

(2016) S. Doerr et al.   Journal of Chemical Theory and Computation

Efficient and Minimal Method to Bias Molecular Simulations with Experimental Data

(2014) Andrew D. White et al.   Journal of Chemical Theory and Computation

Variational Approach to Enhanced Sampling and Free Energy Calculations

(2014) Omar Valsson et al.   PHYSICAL REVIEW LETTERS

i-PI: A Python interface for ab initio path integral molecular dynamics simulations

(2013) Michele Ceriotti et al.   COMPUTER PHYSICS COMMUNICATIONS

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

PLUMED-GUI: An environment for the interactive development of molecular dynamics analysis and biasing scripts

(2013) Toni Giorgino   COMPUTER PHYSICS COMMUNICATIONS

Using collective variables to drive molecular dynamics simulations

(2013) Giacomo Fiorin et al.   MOLECULAR PHYSICS

cp2k: atomistic simulations of condensed matter systems

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

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

(2009) Massimiliano Bonomi et al.   COMPUTER PHYSICS COMMUNICATIONS

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale

(2009) M. J. Harvey et al.   Journal of Chemical Theory and Computation

QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials

(2009) Paolo Giannozzi et al.   JOURNAL OF PHYSICS-CONDENSED MATTER