NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, for example, the Tcl scripting language. The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu.

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Scalable molecular dynamics with NAMD

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Scalable Molecular Dynamics with NAMD

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 thermally activated barrier crossing, the authors report, extend, and interpret much of our current understanding relating to theories of noise-activated escape, for which many of the notable contributions are originating from the communities both of physics and of physical chemistry. Theoretical as well as numerical approaches are discussed for single- and many-dimensional metastable systems (including fields) in gases and condensed phases. The role of many-dimensional transition-state theory is contrasted with Kramers' reaction-rate theory for moderate-to-strong friction; the authors emphasize the physical situation and the close connection between unimolecular rate theory and Kramers' work for weakly damped systems. The rate theory accounting for memory friction is presented, together with a unifying theoretical approach which covers the whole regime of weak-to-moderate-to-strong friction on the same basis (turnover theory). The peculiarities of noise-activated escape in a variety of physically different metastable potential configurations is elucidated in terms of the mean-first-passage-time technique. Moreover, the role and the complexity of escape in driven systems exhibiting possibly multiple, metastable stationary nonequilibrium states is identified. At lower temperatures, quantum tunneling effects start to dominate the rate mechanism. The early quantum approaches as well as the latest quantum versions of Kramers' theory are discussed, thereby providing a description of dissipative escape events at all temperatures. In addition, an attempt is made to discuss prominent experimental work as it relates to Kramers' reaction-rate theory and to indicate the most important areas for future research in theory and experiment.

Reaction-rate theory: fifty years after Kramers

https://www.ks.uiuc.edu/Publications/Papers/PDF/RITZ2000/RITZ2000.pdf

A Model for Photoreceptor-Based Magnetoreception in Birds

http://dasher.wustl.edu/bio5325/reading/curropstrbio-14-76-04.pdf

The protein folding 'speed limit'.

Association reactions involving diffusion in one, two, and three‐dimensional finite domains governed by Smoluchowski‐type equations (e.g., interchain reaction of macromolecules, ligand binding to receptors, repressor–operator association of DNA strand) are shown to be often well described by first‐order kinetics and characterized by an average reaction (passage) time τ. An inhomogeneous differential equation is derived which, for problems with high symmetry, yields τ by simple quadrature without taking recourse to detailed cumbersome time‐dependent solutions of the original Smoluchowski equation. The cases of diffusion and nondiffusion controlled processes are included in the treatment. For reaction processes involving free diffusion and intramolecular chain motion, the validity of the passage time approximation is analyzed.

First passage time approach to diffusion controlled reactions

We develop a first passage time description for the kinetics of reactions involving diffusive barrier crossing in a bistable (and also in a more general) potential, a situation realized, for example, in some photoisomerization processes. In case the reactant is in thermal equilibrium, the first passage times account well for the reaction dynamics as shown by comparison with exact numerical calculations. A simple integral expression for the rate constants is presented. For a case involving a reactant initially far off equilibrium, a two relaxation time description for the particle number N(t) is derived and compared with the results of an ’’exact’’ calculation. This description results from a knowledge of N(t = 0), Ṅ(t = 0), F∞0dt N(t), i.e., the first passage time, and F∞0dt t N(t).

Dynamics of reactions involving diffusive barrier crossing

Pairs of radical ions generated in polar solvents by photoinduced electron transfer either recombine within a few nanoseconds or separate. The (geminate) recombination process is governed by a hyperfine‐coupling‐induced coherent motion of the unpaired electron spins which can be modulated by weak external magnetic fields. The process which also generates the well‐known CIDNP and CIDEP effects is described theoretically by a stochastic Liouville equation comprising for realistic systems a large set of coupled diffusion equations. For the integration of these equations a finite‐difference algorithm with space and time discretization is developed. By comparison with exact solutions of the Liouville equation for model systems, it is demonstrated that an approximate Liouville equation which entails only two coupled diffusion equations for singlet and triplet radical pairs, respectively, suffices to predict the geminate recombination yields accurately. The approximate Liouville equation is employed then to stud...

Theory of the magnetic field modulated geminate recombination of radical ion pairs in polar solvents: Application to the pyrene–N,N‐dimethylaniline system

Pairs of radical ions generated in polar solvents by photoinduced electron transfer either recombine within a few nanoseconds to singlet and triplet products or separate On the basis of recent time‐resolved observations of a magnetic field dependence of the pair recombination a theoretical description of this process is provided The description, similar to the radical pair theory of CIDNP and CIDEP, is founded on a coherent spin motion superimposed on the diffusive motion of the radicals The spin motion is induced by the hyperfine coupling between electron and nuclear spins and can be modulated by low (0–200 G) magnetic fields The spin‐selective recombination of radicals is accounted for by a Feshbach optical potential The diffusion process described by a Smoluchowski operator depends sensitively on the solvent properties For the case of free Brownian motion, simple analytical expressions for the time‐ and magnetic‐field‐dependent recombination yields are derived For the Brownian motion of oppositely charged radical ions a differential–difference approximation is used to demonstrate the dependence of the recombination yields on the viscosity and polarity of the solvent medium as well as on the strength of the hyperfine coupling and on the rate of the electron back transfer

The generation, diffusion, spin motion, and recombination of radical pairs in solution in the nanosecond time domain

It has been suggested that the hydrophilic side groups of proteins can form hydrogen-bonded conductors that transport protons across biomembranes. Based on previous studies of the proton dynamics in ice, a kinetic model for such proton conductors is developed. The steady-state proton current is evaluated as a function of the pH and voltage difference along the conductor. This electrochemical potential is found to determine the mechanism by which the protons are transported. Under acidic conditions the proton current is inversely proportional to the number of side groups composing the conductor and is determined by the rate of injecting a L-Bjerrum orientation fault into the hydrogen-bonded conductor. For small voltages (

Z. Schulten

Papers

First passage time approach to diffusion controlled reactions

Dynamics of reactions involving diffusive barrier crossing

Theory of the magnetic field modulated geminate recombination of radical ion pairs in polar solvents: Application to the pyrene–N,N‐dimethylaniline system

The generation, diffusion, spin motion, and recombination of radical pairs in solution in the nanosecond time domain

Proton conduction in linear hydrogen-bonded systems