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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...

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...

Forty proteins with polypeptide chains of well characterized molecular weights have been studied by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate following the procedure of Shapiro, Vinuela...

Materias / palabras clave: Basis set; Atomic physics; Hydrogen; Exponent; Gaussian; Valence (chemistry); Chemistry; Atom (system on chip); Polarization (electrochemistry); STO-nG basis sets; Atomic orbital; Hydrogen atom

Abstract The molecular structure hypothesis - that a molecule is a collection of atoms linked by a network of bonds - was forged in the crucible of nineteenth-century experimental chemistry and has continued to serve as ...

The chemistry of the coordination polymers has in recent years advanced extensively, affording various architectures, which are constructed from a variety of molecular building blocks with different interactions between ...

Abstract This book provides a practical guide to molecular dynamics and Monte Carlo simulation techniques used in the modelling of simple and complex liquids. Computer simulation is an essential tool in studying the chem...

Phaser is a program for phasing macromolecular crystal structures by both molecular replacement and experimental phasing methods. The novel phasing algorithms implemented in Phaser have been developed using maximum likel...

Starting from the screening in conductors, an algorithm for the accurate calculation of dielectric screening effects in solvents is presented, which leads to rather simple explicit expressions for the screening energy an...

Classical Monte Carlo simulations have been carried out for liquid water in the NPT ensemble at 25 °C and 1 atm using six of the simpler intermolecular potential functions for the water dimer: Bernal–Fowler (BF), SPC,...

The parametrization and testing of the OPLS all-atom force field for organic molecules and peptides are described. Parameters for both torsional and nonbonded energetics have been derived, while the bond stretching and a...

This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, origi...

Adsorptive separation is very important in industry. Generally, the process uses porous solid materials such as zeolites, activated carbons, or silica gels as adsorbents. With an ever increasing need for a more efficient...

Molecular mechanics is powerful for its speed in atomistic simulations, but an accurate force field is required. The Amber ff99SB force field improved protein secondary structure balance and dynamics from earlier force f...

Fil: Noguera, Martín Ezequiel. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Al examinar la estructura tridimensional de proteínas relativamente grandes, se observan regiones donde ...

Gaussian basis sets of quadruple zeta valence quality for Rb-Rn are presented, as well as bases of split valence and triple zeta valence quality for H-Rn. The latter were obtained by (partly) modifying bases developed pr...

Unlike other methods for docking ligands to the rigid 3D structure of a known protein receptor, Glide approximates a complete systematic search of the conformational, orientational, and positional space of the docked lig...

BACKGROUND: The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related are...

Since the classical molecular dynamics simulator LAMMPS was released as an open source code in 2004, it has become a widely-used tool for particle-based modeling of materials at length scales ranging from atomic to mesos...

BACKGROUND: A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de fa...

Molecular structure does not easily identify the intricate noncovalent interactions that govern many areas of biology and chemistry, including design of new materials and drugs. We develop an approach to detect noncovale...

Fil: Pierdominici Sottile, Gustavo. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. En el presente trabajo se utilizó un método mixto clásico-cuántico para estudiar la etapa determi...

AutoDock Vina, a new program for molecular docking and virtual screening, is presented. AutoDock Vina achieves an approximately two orders of magnitude speed-up compared with the molecular docking software previously dev...

Contracted Gaussian basis sets of triple zeta valence (TZV) quality are presented for Li to Kr. The TZV bases are characterized by typically including a single contraction to describe inner shells and three basis functio...