» Articles » PMID: 17212484

Canonical Sampling Through Velocity Rescaling

Overview
Journal J Chem Phys
Specialties Biophysics
Chemistry
Date 2007 Jan 11
PMID 17212484
Citations 4107
Authors
Affiliations
Soon will be listed here.
Abstract

The authors 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. The authors 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 of the thermostat parameter also with regard to the dynamic properties.

Citing Articles

Integrated virtual screening and compound generation targeting H275Y mutation in the neuraminidase gene of oseltamivir-resistant influenza strains.

Khan W, Khan N, Tembhre M, Malik Z, Ansari M, Mishra A Mol Divers. 2025; .

PMID: 40085404 DOI: 10.1007/s11030-025-11163-0.


Structure-guided design of partial agonists at an opioid receptor.

Varga B, Bernhard S, El Daibani A, Zaidi S, Lam J, Aguilar J Nat Commun. 2025; 16(1):2518.

PMID: 40082451 PMC: 11906898. DOI: 10.1038/s41467-025-57734-5.


Bioinspired gel polymer electrolyte for wide temperature lithium metal battery.

Liu S, Tian W, Shen J, Wang Z, Pan H, Kuang X Nat Commun. 2025; 16(1):2474.

PMID: 40075058 PMC: 11904243. DOI: 10.1038/s41467-025-57856-w.


Machine learning-driven molecular dynamics unveils a bulk phase transformation driving ammonia synthesis on barium hydride.

Tosello Gardini A, Raucci U, Parrinello M Nat Commun. 2025; 16(1):2475.

PMID: 40074737 PMC: 11903671. DOI: 10.1038/s41467-025-57688-8.


Oxygen Vacancies on Hydrated Anatase (101) Surfaces: Insights from Classical and Ab Initio Molecular Dynamics Simulations.

Grote F, Lyubartsev A Nanomaterials (Basel). 2025; 15(5).

PMID: 40072167 PMC: 11901595. DOI: 10.3390/nano15050364.