Scalable molecular dynamics with NAMD

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1996 • 54,630 citations

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

1993 • 26,634 citations

Computer Simulation of Liquids

2017 • 20,627 citations

Canonical dynamics: Equilibrium phase-space distributions

1985 • 20,411 citations

A smooth particle mesh Ewald method

1995 • 20,143 citations

Computer Simulation of Liquids

1988 • 15,963 citations

All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins

1998 • 13,827 citations

GROMACS: A message-passing parallel molecular dynamics implementation

1995 • 9,228 citations

Mathematical Methods of Classical Mechanics

1989 • 8,994 citations

THE UBIQUITIN SYSTEM

1998 • 8,360 citations

Understanding Molecular Simulation: From Algorithms to Applications

2001 • 6,276 citations

THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method

1992 • 6,255 citations

Die Berechnung optischer und elektrostatischer Gitterpotentiale

1921 • 5,649 citations

Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling

1977 • 5,626 citations

Understanding Molecular Simulation: From Algorithms to Applications

1997 • 5,260 citations

Nonequilibrium Equality for Free Energy Differences

1997 • 4,832 citations

A new force field for molecular mechanical simulation of nucleic acids and proteins

1984 • 4,553 citations

Replica-exchange molecular dynamics method for protein folding

1999 • 4,335 citations

Constant pressure molecular dynamics simulation: The Langevin piston method

1995 • 4,126 citations

Numerical Initial Value Problems in Ordinary Differential Equations

1973 • 4,016 citations

Numerical Initial Value Problems in Ordinary Differential Equations

1972 • 3,569 citations

Reversible multiple time scale molecular dynamics

1992 • 3,392 citations

Water conduction through the hydrophobic channel of a carbon nanotube

2001 • 3,341 citations

High-Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases

1954 • 2,894 citations

NAMD2: Greater Scalability for Parallel Molecular Dynamics

1999 • 2,396 citations

Computer Simulation Using Particles

1981 • 2,204 citations

Numerical methods

1974 • 1,767 citations

Geometric Numerical Integration

2002 • 1,749 citations

Statistical Physics II

1991 • 1,664 citations

Tcl and the Tk Toolkit

1994 • 1,660 citations

The calculation of the potential of mean force using computer simulations

1995 • 1,640 citations

Statistical Physics II: Nonequilibrium Statistical Mechanics

2003 • 1,576 citations

Simulation of electrostatic systems in periodic boundary conditions. I. Lattice sums and dielectric constants

1980 • 1,309 citations

Equilibrium free-energy differences from nonequilibrium measurements: A master-equation approach

1997 • 1,275 citations

Equilibrium Information from Nonequilibrium Measurements in an Experimental Test of Jarzynski's Equality

2002 • 1,187 citations

<scp>AMBER</scp>: Assisted model building with energy refinement. A general program for modeling molecules and their interactions

1981 • 1,120 citations

Components of ubiquitin-protein ligase system. Resolution, affinity purification, and role in protein breakdown.

1983 • 1,105 citations

Calculating free energies using average force

2001 • 1,026 citations

Steered molecular dynamics and mechanical functions of proteins

2001 • 1,002 citations

Constant-pressure equations of motion

1986 • 914 citations

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

1996 • 913 citations

Control of the Selectivity of the Aquaporin Water Channel Family by Global Orientational Tuning

2002 • 883 citations

Calculating potentials of mean force from steered molecular dynamics simulations

2004 • 871 citations

Lecture notes in computational science and engineering

2010 • 822 citations

Crystal Structure of the Lactose Operon Repressor and Its Complexes with DNA and Inducer

1996 • 781 citations

Molecular dynamics study of unbinding of the avidin-biotin complex

1997 • 774 citations

Free energy calculation from steered molecular dynamics simulations using Jarzynski’s equality

2003 • 766 citations

Protein Data Bank

1984 • 731 citations

Imaging α-Hemolysin with Molecular Dynamics: Ionic Conductance, Osmotic Permeability, and the Electrostatic Potential Map

2005 • 651 citations

Computational Statistical Mechanics

1991 • 641 citations

Generalized Verlet Algorithm for Efficient Molecular Dynamics Simulations with Long-range Interactions

1991 • 603 citations

Stochastic boundary conditions for molecular dynamics simulations of ST2 water

1984 • 596 citations

Genetic Switch

2008 • 590 citations

Force-Clamp Spectroscopy Monitors the Folding Trajectory of a Single Protein

2004 • 539 citations

NAMD: a Parallel, Object-Oriented Molecular Dynamics Program

1996 • 533 citations

The mechanical stability of ubiquitin is linkage dependent

2003 • 475 citations

F<scp>ROM</scp> F<scp>OLDING</scp> T<scp>HEORIES TO</scp> F<scp>OLDING</scp> P<scp>ROTEINS</scp>: A Review and Assessment of Simulation Studies of Protein Folding and Unfolding

2001 • 472 citations

Overcoming free energy barriers using unconstrained molecular dynamics simulations

2004 • 443 citations

Parallel programming

1998 • 419 citations

Multilevel matrix multiplication and fast solution of integral equations

1990 • 417 citations

Steered Molecular Dynamics

1999 • 406 citations

Effect of Electrostatic Force Truncation on Interfacial and Transport Properties of Water

1996 • 376 citations

Energetics of glycerol conduction through aquaglyceroporin GlpF

2002 • 359 citations

Steered molecular dynamics investigations of protein function

2001 • 352 citations

Non-Hamiltonian molecular dynamics: Generalizing Hamiltonian phase space principles to non-Hamiltonian systems

2001 • 351 citations

Treatment of electrostatic effects in macromolecular modeling

1989 • 350 citations

Theory and Simulation of Water Permeation in Aquaporin-1

2004 • 340 citations

Pressure-Induced Water Transport in Membrane Channels Studied by Molecular Dynamics

2002 • 331 citations

The mechanism of ubiquitin activating enzyme. A kinetic and equilibrium analysis.

1982 • 324 citations

Crystal Structure of lac Repressor Core Tetramer and Its Implications for DNA Looping

1995 • 290 citations

The Key Event in Force-Induced Unfolding of Titin’s Immunoglobulin Domains

2000 • 284 citations

Molecular Dynamics Simulations of a Polyalanine Octapeptide under Ewald Boundary Conditions: Influence of Artificial Periodicity on Peptide Conformation

2000 • 279 citations

Hidden Thermodynamics of Mutant Proteins: A Molecular Dynamics Analysis

1989 • 275 citations

Steered molecular dynamics simulations of force-induced protein domain unfolding

1999 • 274 citations

Computational Molecular Dynamics: Challenges, Methods, Ideas

1999 • 269 citations

In Search of the Hair-Cell Gating Spring

2005 • 269 citations

Backward Error Analysis for Numerical Integrators

1999 • 248 citations

The effects of truncating long‐range forces on protein dynamics

1989 • 243 citations

An algorithm for the simulation of condensed matter which grows as the 3/2 power of the number of particles

1988 • 239 citations

The effect of point mutations on the free energy of transmembrane α-helix dimerization

1997 • 235 citations

Collective Diffusion Model for Water Permeation through Microscopic Channels

2004 • 220 citations

Sur une propri�t� de la loi de Gau�

1939 • 199 citations

The lac Operon

1996 • 195 citations

The calculation of free-energy differences by constrained molecular-dynamics simulations

1998 • 180 citations

Unbinding of Retinoic Acid from its Receptor Studied by Steered Molecular Dynamics

1999 • 178 citations

Electrostatic Tuning of Permeation and Selectivity in Aquaporin Water Channels

2003 • 166 citations

Dynamics of reactions involving diffusive barrier crossing

1981 • 163 citations

Binding pathway of retinal to bacterio-opsin: a prediction by molecular dynamics simulations

1997 • 158 citations

Constant-temperature free energy surfaces for physical and chemical processes

1993 • 157 citations

Gating of MscL Studied by Steered Molecular Dynamics

2003 • 157 citations

Multiple grid methods for classical molecular dynamics

2002 • 155 citations

The Mechanism of Glycerol Conduction in Aquaglyceroporins

2001 • 150 citations

Steered Molecular Dynamics Simulation of the Rieske Subunit Motion in the Cytochrome bc1 Complex

1999 • 148 citations

Insights into the Recognition and Association of Transmembrane α-Helices. The Free Energy of α-Helix Dimerization in Glycophorin A

2005 • 145 citations

Insights into the Molecular Mechanism of Rotation in the Fo Sector of ATP Synthase

2004 • 141 citations

Computational Studies of Membrane Channels

2004 • 140 citations

Structural dynamics of the lac repressor–DNA complex revealed by a multiscale simulation

2005 • 138 citations

Langevin dynamics in constant pressure extended systems

2004 • 136 citations

Reconstructing Potentials of Mean Force through Time Series Analysis of Steered Molecular Dynamics Simulations

1999 • 136 citations

Influence of Artificial Periodicity and Ionic Strength in Molecular Dynamics Simulations of Charged Biomolecules Employing Lattice-Sum Methods

2003 • 131 citations

Verlet-I/R-RESPA/Impulse is Limited by Nonlinear Instabilities

2003 • 117 citations

Steered Molecular Dynamics Studies of Titin I1 Domain Unfolding

2002 • 114 citations

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

1997 • 106 citations

Mechanisms of Selectivity in Channels and Enzymes Studied with Interactive Molecular Dynamics

2003 • 97 citations

Molecular dynamics study of aquaporin‐1 water channel in a lipid bilayer

2001 • 96 citations

Structural Insights into How the MIDAS Ion Stabilizes Integrin Binding to an RGD Peptide under Force

2004 • 85 citations

Multiscale Method for Simulating Protein-DNA Complexes

2004 • 76 citations

CHARM++

1996 • 75 citations

Bacterial ion channels and their eukaryotic homologues

2001 • 71 citations

Influence of cut-off truncation and artificial periodicity of electrostatic interactions in molecular simulations of solvated ions: A continuum electrostatics study

2003 • 70 citations

Fluorescence Resonance Energy Transfer over ∼130 Basepairs in Hyperstable Lac Repressor-DNA Loops

2003 • 70 citations

Forced Detachment of the CD2-CD58 Complex

2003 • 65 citations

Analysis of a few numerical integration methods for the Langevin equation

2003 • 59 citations

Binding of the estrogen receptor to DNA. The role of waters

1997 • 57 citations

Extraction of Lipids from Phospholipid Membranes by Steered Molecular Dynamics

1997 • 56 citations

MDScope — a visual computing environment for structural biology

1995 • 51 citations

Structural Basis for Cooperative DNA Binding by CAP and Lac Repressor

2004 • 48 citations

Modelling DNA loops using continuum and statistical mechanics One contribution of 16 to a Theme ‘The mechanics of DNA’

2004 • 38 citations

The notion of error in Langevin dynamics. I. Linear analysis

1996 • 28 citations

Computer Modeling of Force-Induced Titin Domain Unfolding

2000 • 24 citations

Elastic Filaments of the Cell

2000 • 22 citations

Protein Flexibility and Folding

2001 • 6 citations

Avoiding Algorithmic Obfuscation in a Message-Driven Parallel MD Code

1999 • 6 citations

Towards an Understanding of Membrane Channels

2014 • 4 citations

Parallel and Distributed Computing for Symbolic and Irregular Applications

2000 • 2 citations