Best bang for your buck: GPU nodes for GROMACS biomolecular simulations

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

A flexible algorithm for calculating pair interactions on SIMD architectures

(2013) Szilárd Páll et al.   COMPUTER PHYSICS COMMUNICATIONS

Lennard-Jones Lattice Summation in Bilayer Simulations Has Critical Effects on Surface Tension and Lipid Properties

(2013) Christian L. Wennberg et al.   Journal of Chemical Theory and Computation

Energy barriers and driving forces in tRNA translocation through the ribosome

(2013) Lars V Bock et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

An overview of the Amber biomolecular simulation package

(2012) Romelia Salomon-Ferrer et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Implementing molecular dynamics on hybrid high performance computers – Particle–particle particle-mesh

(2011) W. Michael Brown et al.   COMPUTER PHYSICS COMMUNICATIONS

Optimization of parameters for molecular dynamics simulation using smooth particle-mesh Ewald in GROMACS 4.5

(2011) Mark J. Abraham et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Systematic benchmarking of large molecular dynamics simulations employing GROMACS on massive multiprocessing facilities

(2010) Christian C. Gruber et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale

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

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation