Advanced search
Publication Cover
Molecular Simulation Volume 13, 1994 - Issue 6
Submit an article Journal homepage
143
Views
50
CrossRef citations to date
0
Altmetric
Original Articles

A Non-Iterative Matrix Method for Constraint Molecular Dynamics Simulations

Makoto Yoneya Hitachi Research Laboratory, Hitachi, Ltd., 7-1-1 Omika, Hitachi, Ibaraki, 319-12, Japan
,
H. J. C. Berendsen Laboratory of Biophysical Chemistry, Universtiy of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
&
Kootaro Hirasawa Hitachi Research Laboratory, Hitachi, Ltd., 7-1-1 Omika, Hitachi, Ibaraki, 319-12, Japan; Department of Electrical Engineering, Kyusyu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812, Japan
Pages 395-405 | Received 01 Feb 1994, Accepted 01 May 1994, Published online: 23 Sep 2006
 
Sample our Physical Sciences journals, sign in here to start your FREE access for 14 days

Abstract

A non-iterative version of the matrix method which can be easily vectorised and parallelized is presented. The original matrix method, which is conceptually identical to the familiar SHAKE algorithm, is shown to be non-iterative when incorporated with the Verlet and leap-frog integration schemes with the same constraint error order as the (local) error order of the accompanying integration schemes. The method is checked by test simulations with n-butane and the liquid crystal moleculae 5CB (4-n-pentyl-4′-cyanobiphenyl) in which its effectiveness is demonstrated.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Order Reprints Request Corporate Permissions

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

Request Academic Permissions

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.

Related Research Data

A computational study on the usability of amino acid-functionalised nitrogen-doped graphene oxides as temperature-responsive drug delivery systems.
Source: Taylor & Francis
A LEAP-FROG ALGORITHM FOR STOCHASTIC DYNAMICS
Source: Informa UK Limited
Molecular dynamics with constraints
Source: Elsevier BV
Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes
Source: Elsevier BV
New algorithm for constrained molecular-dynamics simulation of liquid benzene and naphthalene
Source: Informa UK Limited
Systolic Loop Methods for Molecular Dynamics Simulation, Generalised for Macromolecules
Source: Informa UK Limited
Vector and parallel algorithms for the molecular dynamics simulation of macromolecules on shared‐memory computers
Source: Wiley
Multi-colour algorithms in molecular simulation: vectorisation and parallelisation of internal forces and constraints
Source: Elsevier BV
Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations
Source: Elsevier BV
Free energy landscapes of prototropic tautomerism in pyridoxal 5′‐phosphate schiff bases at the active site of an enzyme in aqueous medium
Source: Wiley
Molecular dynamics on a distributed-memory multiprocessor
Source: Wiley

Linking provided by 

Related research

People also read lists articles that other readers of this article have read.

Recommended articles lists articles that we recommend and is powered by our AI driven recommendation engine.

Cited by lists all citing articles based on Crossref citations.
Articles with the Crossref icon will open in a new tab.