CHARMM: the biomolecular simulation program

BR Brooks, CL Brooks III… - Journal of …, 2009 - Wiley Online Library
Abstract CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and
widely used molecular simulation program. It has been developed over the last three …

Reaction-rate theory: fifty years after Kramers

P Hänggi, P Talkner, M Borkovec - Reviews of modern physics, 1990 - APS
The calculation of rate coefficients is a discipline of nonlinear science of importance to much
of physics, chemistry, engineering, and biology. Fifty years after Kramers' seminal paper on …

Current status of transition-state theory

DG Truhlar, BC Garrett… - The Journal of physical …, 1996 - ACS Publications
We present an overview of the current status of transition-state theory and its
generalizations. We emphasize (i) recent improvements in available methodology for …

Langevin dynamics of peptides: The frictional dependence of isomerization rates of N‐acetylalanyl‐N′‐methylamide

RJ Loncharich, BR Brooks… - … : Original Research on …, 1992 - Wiley Online Library
The rate constant for the transition between the equatorial and axial conformations of N‐
acetylalanyl‐N′‐methylamide has been determined from Langevin dynamics (LD) …

Femtosecond solvation dynamics of water

R Jimenez, GR Fleming, PV Kumar, M Maroncelli - Nature, 1994 - nature.com
THE timescale of the response of solvent molecules to electronic rearrangement of solute
molecules has a critical influence on the rates of chemical reactions in liquids1–10. In …

Quantum Brownian motion: The functional integral approach

H Grabert, P Schramm, GL Ingold - Physics reports, 1988 - Elsevier
The quantum mechanical dynamics of a particle coupled to a heat bath is treated by
functional integral methods and a generalization of the Feynman-Vernon influence …

The protein folding 'speed limit'

J Kubelka, J Hofrichter, WA Eaton - Current opinion in structural biology, 2004 - Elsevier
How fast can a protein possibly fold? This question has stimulated experimentalists to seek
fast folding proteins and to engineer them to fold even faster. Proteins folding at or near the …

Extending the time scale in atomistic simulation of materials

AF Voter, F Montalenti… - Annual review of materials …, 2002 - annualreviews.org
▪ Abstract Obtaining a good atomistic description of diffusion dynamics in materials has been
a daunting task owing to the time-scale limitations of the molecular dynamics method. We …

Enhancing important fluctuations: Rare events and metadynamics from a conceptual viewpoint

O Valsson, P Tiwary, M Parrinello - Annual review of physical …, 2016 - annualreviews.org
Atomistic simulations play a central role in many fields of science. However, their usefulness
is often limited by the fact that many systems are characterized by several metastable states …

A method for accelerating the molecular dynamics simulation of infrequent events

AF Voter - The Journal of chemical physics, 1997 - pubs.aip.org
For infrequent-event systems, transition state theory (TST) is a powerful approach for
overcoming the time scale limitations of the molecular dynamics (MD) simulation method …