The Molecular Dynamics Replicated Data Model implements a parallel computer program that uses a 3D Lennard-Jones potential truncated at a distance of three molecular diameters. Each thread computes a portion of the force on each atom and these contributions are summed to compute the total acceleration using the Verlet ODE algorithm. Allocating memory for each thread's avoids the problem of parallel threads simultaneously writing to array elements.
The Molecular Dynamics Replicated Data Model was developed using the Easy Java Simulations (EJS) modeling tool. It is distributed as a ready-to-run (compiled) Java archive.
Please note that this resource requires
at least version 1.7 of Java (JRE).
Parallel Programming Tutorial
A step-by-step introduction to parallel programming in Java using EJS. download 2083kb .pdf
Last Modified: December 22, 2017
Molecular Dynamics Replicated Data Source Code
The source code zip archive contains an XML representation of the Molecular Dynamics Replicated Data Model. Unzip this archive in your Ejs workspace to compile and run this model using EJS. download 52kb .zip
Last Modified: October 19, 2017
previous versions
W. Christian, Computer Program MOLECULAR DYNAMICS REPLICATED DATA MODEL, Version 1.0 (2013), WWW Document, (https://www.compadre.org/Repository/document/ServeFile.cfm?ID=12987&DocID=3559).
W. Christian, Computer Program MOLECULAR DYNAMICS REPLICATED DATA MODEL, Version 1.0 (2013), <https://www.compadre.org/Repository/document/ServeFile.cfm?ID=12987&DocID=3559>.
Christian, W. (2013). Molecular Dynamics Replicated Data Model (Version 1.0) [Computer software]. Retrieved December 8, 2024, from https://www.compadre.org/Repository/document/ServeFile.cfm?ID=12987&DocID=3559
Christian, Wolfgang. "Molecular Dynamics Replicated Data Model." Version 1.0. https://www.compadre.org/Repository/document/ServeFile.cfm?ID=12987&DocID=3559 (accessed 8 December 2024).
%A Wolfgang Christian %T Molecular Dynamics Replicated Data Model %D August 30, 2013 %U https://www.compadre.org/Repository/document/ServeFile.cfm?ID=12987&DocID=3559 %O 1.0 %O application/java
%0 Computer Program %A Christian, Wolfgang %D August 30, 2013 %T Molecular Dynamics Replicated Data Model %7 1.0 %8 August 30, 2013 %U https://www.compadre.org/Repository/document/ServeFile.cfm?ID=12987&DocID=3559
Disclaimer: ComPADRE offers citation styles as a guide only. We cannot offer interpretations about citations as this is an automated procedure. Please refer to the style manuals in the Citation Source Information area for clarifications.
The Easy Java Simulations Modeling and Authoring Tool is needed to explore the computational model used in the Molecular Dynamics Replicated Data Model.
1 source code document is available
Record Link
Save to my folders
