scispace - formally typeset
Open AccessJournal ArticleDOI

Canonical sampling through velocity-rescaling

TLDR
In this paper, a new molecular dynamics algorithm for sampling the canonical distribution is presented, in which the velocities of all the particles are rescaled by a properly chosen random factor.
Abstract
We present a new molecular dynamics algorithm for sampling the canonical distribution. In this approach the velocities of all the particles are rescaled by a properly chosen random factor. The algorithm is formally justified and it is shown that, in spite of its stochastic nature, a quantity can still be defined that remains constant during the evolution. In numerical applications this quantity can be used to measure the accuracy of the sampling. We illustrate the properties of this new method on Lennard-Jones and TIP4P water models in the solid and liquid phases. Its performance is excellent and largely independent on the thermostat parameter also with regard to the dynamic properties.

read more

Citations
More filters

Análisis por dinámica molecular de propiedades tensoactivas de lipopéptidos producidos por Bacillus spp. para su potencial uso en recuperación mejorada de petróleo

TL;DR: In this article, a set of similares of two lipopeptidos protonados by Bacillus spp. were used to evaluate the effect of the surfactina iC15 on the tensor de presion of the sistema hexadecano-agua.
Journal ArticleDOI

Omicron: A Heavily Mutated SARS-CoV-2 Variant Exhibits Stronger Binding to ACE2 and Potently Escapes Approved COVID-19 Therapeutic Antibodies

TL;DR: Investigating the binding strength of Omicron with ACE2 and monoclonal antibodies that are either approved by the FDA for COVID-19 therapy or undergoing phase III clinical trials suggests that the Spike mutations prudently devised by the virus facilitate the receptor binding, weakening the mAbs binding to escape the immune response.
Journal ArticleDOI

Insights into the activity of single-atom Fe-N-C catalysts for oxygen reduction reaction

TL;DR: In this paper , the authors provided a model to understand the ORR activity of Fe-N4 site from the spatial structure and energy level of the frontier orbitals by density functional theory calculations.
Journal ArticleDOI

AI-based structure prediction empowers integrative structural analysis of human nuclear pores

TL;DR: This study used artificial intelligence (AI)–based prediction to generate an extensive repertoire of structural models of human NUPs and their subcomplexes that cover various domains and interfaces that so far remained structurally uncharacterized and increases the structural coverage of the human NPC scaffold by about twofold.
Related Papers (5)
Trending Questions (1)
What is the most cost effective thermostat setting?

Its performance is excellent and largely independent of the thermostat parameter also with regard to the dynamic properties.