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

VMD: Visual molecular dynamics

1996 • 54,630 citations

Canonical dynamics: Equilibrium phase-space distributions

1985 • 20,411 citations

A unified formulation of the constant temperature molecular dynamics methods

1984 • 16,207 citations

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1986 • 14,074 citations

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

1998 • 13,827 citations

Understanding Molecular Simulation: From Algorithms to Applications

1997 • 5,260 citations

Nonequilibrium Equality for Free Energy Differences

1997 • 4,832 citations

Statistical Mechanics of Fluid Mixtures

1935 • 3,283 citations

Optimized Monte Carlo data analysis

1989 • 2,506 citations

NAMD2: Greater Scalability for Parallel Molecular Dynamics

1999 • 2,396 citations

Thermodynamics and an Introduction to Thermostatistics

1987 • 2,317 citations

Monte Carlo free energy estimates using non-Boltzmann sampling: Application to the sub-critical Lennard-Jones fluid

1974 • 1,340 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

Steered molecular dynamics and mechanical functions of proteins

2001 • 1,002 citations

Free energy reconstruction from nonequilibrium single-molecule pulling experiments

2001 • 935 citations

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1997 • 774 citations

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1940 • 513 citations

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2001 • 485 citations

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2002 • 359 citations

Thermodynamics and an Introduction to Thermostatistics, 2nd ed.

1998 • 355 citations

Steered molecular dynamics investigations of protein function

2001 • 352 citations

Forced unfolding of the fibronectin type III module reveals a tensile molecular recognition switch

1999 • 269 citations

Fast-growth thermodynamic integration: Error and efficiency analysis

2001 • 248 citations

Sur une propri�t� de la loi de Gau�

1939 • 199 citations

Identifying Unfolding Intermediates of FN-III10 by Steered Molecular Dynamics

2002 • 177 citations

Theory of a Systematic Computational Error in Free Energy Differences

2002 • 163 citations

Reconstructing potential energy functions from simulated force-induced unbinding processes

1997 • 155 citations

Solvent effects on the energy landscapes and folding kinetics of polyalanine

2001 • 146 citations

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

1999 • 136 citations

A “fast growth” method of computing free energy differences

2001 • 136 citations

Systematic errors in free energy perturbation calculations due to a finite sample of configuration space: sample-size hysteresis

1991 • 133 citations

Simple analysis of noise and hysteresis in (slow-growth) free energy simulations

1991 • 114 citations

Steered Molecular Dynamics Studies of Titin I1 Domain Unfolding

2002 • 114 citations

Overcoming finite-sampling errors in fast-switching free-energy estimates: extrapolative analysis of a molecular system

2002 • 70 citations

Forced Detachment of the CD2-CD58 Complex

2003 • 65 citations

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2003 • 51 citations