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GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules. It provides a rich set of calculation types, preparation and analysis too...

Abstract We generalize the method proposed by Gelman and Rubin (1992a) for monitoring the convergence of iterative simulations by comparing between and within variances of multiple chains, in order to obtain a family of ...

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...

In the molecular dynamics simulation method for fluids, the equations of motion for a collection of particles in a fixed volume are solved numerically. The energy, volume, and number of particles are constant for a parti...

Adequate initial configurations for molecular dynamics simulations consist of arrangements of molecules distributed in space in such a way to approximately represent the system's overall structure. In order that the simu...

Esta obra ha desarrollado el Laboratorio de Física a través de Simulación Computacional, como una herramienta pedagógica que toma las simulaciones de phET Interactive Simulations (University of Colorado Boulder) para...

El presente libro, desarrollado en el marco del proyecto Accurate Simulations of Fretting Fatigue Frictional Behavior de la Universidad Tecnológica de Pereira, aborda el análisis estructural de componentes sometidos a ...

We present ab initio quantum-mechanical molecular-dynamics simulations of the liquid-metal--amorphous-semiconductor transition in Ge. Our simulations are based on (a) finite-temperature density-functional theory of the o...

New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (b...

The fifth phase of the Coupled Model Intercomparison Project (CMIP5) will produce a state-of-the- art multimodel dataset designed to advance our knowledge of climate variability and climate change. Researchers worldwide ...

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...

BACKGROUND: Usually the researchers performing meta-analysis of continuous outcomes from clinical trials need their mean value and the variance (or standard deviation) in order to pool data. However, sometimes the publis...

Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems. Here, we present a new implementation of our molecular simulation toolkit GROMACS whi...

Recent advances in hardware and software have enabled increasingly long molecular dynamics (MD) simulations of biomolecules, exposing certain limitations in the accuracy of the force fields used for such simulations and ...

The Gibbs sampler, the algorithm of Metropolis and similar iterative simulation methods are potentially very helpful for summarizing multivariate distributions. Used naively, however, iterative simulation can give mislea...

Abstract. By coordinating the design and distribution of global climate model simulations of the past, current, and future climate, the Coupled Model Intercomparison Project (CMIP) has become one of the foundational elem...

Prior to the twentieth century, theories of knowledge were inherently perceptual. Since then, developments in logic, statistics, and programming languages have inspired amodal theories that rest on principles fundamental...

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...