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There are now a wide variety of packages for electronic structure calculations, each of which differs in the algorithms implemented and the output format. Many computational chemistry algorithms are only available to use...

Subjects / keywords: Computer science; Mathematics; Set theory; Problems, exercises, etc; Algorithms; Logic, Symbolic and mathematical; Problems and exercises; Electronic books

A novel and robust automated docking method that predicts the bound conformations of flexible ligands to macromolecular targets has been developed and tested, in combination with a new scoring function that estimates the...

Abstract An analytical algorithm, called SETTLE, for resetting the positions and velocities to satisfy the holonomic constraints on the rigid water model is presented. This method is still based on the Cartesian coordina...

In this article, we present a new LINear Constraint Solver (LINCS) for molecular simulations with bond constraints. The algorithm is inherently stable, as the constraints themselves are reset instead of derivatives of th...

Abstract The Weighted Histogram Analysis Method (WHAM), an extension of Ferrenberg and Swendsen's Multiple Histogram Technique, has been applied for the first time on complex biomolecular Hamiltonians. The method is pres...

Subjects / keywords: TREMBLAY, JEAN-PAUL; MCGRAW-HILL; 005.113 T789in

Subjects / keywords: Python (Computer program language); Data structures (Computer science); Computer algorithms

Subjects / keywords: Text processing (Computer science); Genetic algorithms; Computational linguistics

Subjects / keywords: Computer algorithms; Databases; Data structures (Computer science); Structured programming

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 lo...