Journal ArticleDOI
Constant-pressure equations of motion
TLDR
Some of the differences among several alternative formulations of constant-pressure molecular dynamics are described, which all agree in the large-system limit, but differ for small systems.Abstract:
Some of the differences among several alternative formulations of constant-pressure molecular dynamics are described. The formulations all agree in the large-system limit, but differ for small systems.read more
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Journal ArticleDOI
Scalable molecular dynamics with NAMD
James C. Phillips,Rosemary Braun,Wei Wang,James C. Gumbart,Emad Tajkhorshid,Elizabeth Villa,Christophe Chipot,Robert D. Skeel,Laxmikant V. Kale,Klaus Schulten +9 more
TL;DR: NAMD as discussed by the authors is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems that scales to hundreds of processors on high-end parallel platforms, as well as tens of processors in low-cost commodity clusters, and also runs on individual desktop and laptop computers.
Journal ArticleDOI
Constant pressure molecular dynamics algorithms
TL;DR: In this paper, a modularly invariant equations of motion are derived that generate the isothermal-isobaric ensemble as their phase space averages, and the resulting methods are tested on two problems, a particle in a one-dimensional periodic potential and a spherical model of C60 in the solid/fluid phase.
Journal ArticleDOI
The Atomic Simulation Environment - A Python library for working with atoms
Ask Hjorth Larsen,Ask Hjorth Larsen,Jens Jørgen Mortensen,Jakob Blomqvist,Ivano E. Castelli,Rune Christensen,Marcin Dulak,Jesper Friis,Michael N. Groves,Bjørk Hammer,Cory Hargus,Eric D. Hermes,Paul C. Jennings,Peter Bjerre Jensen,James R. Kermode,John R. Kitchin,Esben L. Kolsbjerg,Joseph Kubal,Kristen Kaasbjerg,Steen Lysgaard,Jon Bergmann Maronsson,Tristan Maxson,Thomas Olsen,Lars Pastewka,Andrew A. Peterson,Carsten Rostgaard,Jakob Schiøtz,Ole Schütt,Mikkel Strange,Kristian Sommer Thygesen,Tejs Vegge,Lasse B. Vilhelmsen,Michael Walter,Zhenhua Zeng,Karsten Wedel Jacobsen +34 more
TL;DR: The atomic simulation environment (ASE) provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.
Journal ArticleDOI
Scalable molecular dynamics on CPU and GPU architectures with NAMD.
James C. Phillips,David J. Hardy,Julio D.C. Maia,John E. Stone,João V. Ribeiro,Rafael C. Bernardi,Ronak Buch,Giacomo Fiorin,Jérôme Hénin,Wei Jiang,Ryan McGreevy,Marcelo C. R. Melo,Brian K. Radak,Robert D. Skeel,Abhishek Singharoy,Yi Wang,Benoît Roux,Aleksei Aksimentiev,Zaida Luthey-Schulten,Laxmikant V. Kale,Klaus Schulten,Christophe Chipot,Emad Tajkhorshid +22 more
TL;DR: The main features of NAMD are reviewed, including the variety of options offered by NAMD for enhanced-sampling simulations aimed at determining free-energy differences of either alchemical or geometrical transformations and their applicability to specific problems.