NAMD2: Greater Scalability for Parallel Molecular Dynamics

VMD: Visual molecular dynamics

1996 • 54,630 citations

Fast Parallel Algorithms for Short-Range Molecular Dynamics

1995 • 39,531 citations

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

1993 • 26,634 citations

A smooth particle mesh Ewald method

1995 • 20,143 citations

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

1977 • 19,896 citations

Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules

1967 • 8,657 citations

A fast algorithm for particle simulations

1987 • 4,825 citations

A hierarchical O(N log N) force-calculation algorithm

1986 • 3,425 citations

Reversible multiple time scale molecular dynamics

1992 • 3,392 citations

Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations

1983 • 2,842 citations

Computer Simulation Using Particles

1981 • 2,204 citations

Tcl and the Tk Toolkit

1994 • 1,660 citations

Reevaluating Amdahl's law

1988 • 1,385 citations

The X-ray crystal structure of the membrane protein prostaglandin H2 synthase-1

1994 • 1,263 citations

PVM: A framework for parallel distributed computing

1990 • 1,193 citations

Crystal structure of the RAR-γ ligand-binding domain bound to all-trans retinoic acid

1995 • 1,085 citations

Free Energy Via Molecular Simulation: Applications to Chemical and Biomolecular Systems

1989 • 1,052 citations

Ligand Binding: Molecular Mechanics Calculation of the Streptavidin-Biotin Rupture Force

1996 • 913 citations

CHARM++

1993 • 844 citations

Prostaglandin Endoperoxide H Synthases-1 and -2

1996 • 721 citations

Unfolding of Titin Immunoglobulin Domains by Steered Molecular Dynamics Simulation

1998 • 692 citations

NAMD: a Parallel, Object-Oriented Molecular Dynamics Program

1996 • 533 citations

Parallel programming

1998 • 419 citations

Steered Molecular Dynamics

1999 • 406 citations

Comments on P3M, FMM, and the Ewald method for large periodic Coulombic systems

1996 • 385 citations

[32] Reconstitution of high-density lipoproteins

1986 • 316 citations

Isoefficiency: measuring the scalability of parallel algorithms and architectures

1993 • 301 citations

Computational Molecular Dynamics: Challenges, Methods, Ideas

1999 • 269 citations

A Comparison of Particle-Particle, Particle-Mesh and Ewald Methods for Calculating Electrostatic Interactions in Periodic Molecular Systems

1994 • 202 citations

Predicting the structure of apolipoprotein A-I in reconstituted high-density lipoprotein disks

1997 • 138 citations

A new parallel method for molecular dynamics simulation of macromolecular systems

1996 • 132 citations

Large Scale Molecular Dynamics on Parallel Computers using the Link-cell Algorithm

1991 • 108 citations

Difficulties with multiple time stepping and fast multipole algorithm in molecular dynamics

1997 • 106 citations

Histone structure and function

1991 • 90 citations

Nuclear Hormone Receptors

2007 • 81 citations

Converse: an interoperable framework for parallel programming

2002 • 76 citations

CHARM++

1996 • 75 citations

Isoefficiency: measuring the scalability of parallel algorithms and architectures

1995 • 74 citations

Simulations of Macromolecules by Multiple Time-Step Methods

1995 • 71 citations

A domain decomposition parallel processing algorithm for molecular dynamics simulations of polymers

1994 • 63 citations

FAMUSAMM: An algorithm for rapid evaluation of electrostatic interactions in molecular dynamics simulations

1997 • 57 citations

Parallelizing molecular dynamics programs for distributed-memory machines

1995 • 57 citations

FAMUSAMM: An algorithm for rapid evaluation of electrostatic interactions in molecular dynamics simulations.

1997 • 53 citations

MDScope — a visual computing environment for structural biology

1995 • 51 citations

A domain decomposition parallel processing algorithm for molecular dynamics simulations of systems of arbitrary connectivity

1997 • 50 citations

Parallelizing molecular dynamics using spatial decomposition

2002 • 44 citations

A portable distributed implementation of the parallel multipole tree algorithm

2002 • 35 citations

Reevaluating Amdahl's law

1995 • 32 citations

Efficient Parallel Implementation of Molecular Dynamics on a Toroidal Network. Part II. Multi-particle Potentials

1993 • 30 citations

Structured dagger: A coordination language for Message-Driven Programming

1996 • 29 citations

A highly portable parallel implementation of AMBER4 using the message passing interface standard

1995 • 27 citations

Advanced Algorithms for Molecular Dynamics Simulation

1995 • 17 citations

Multiparadigm, multilingual interoperability: Experience with converse

1998 • 17 citations

MDScope — A Visual Computing Environment for Structural Biology

1995 • 6 citations