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 1.6 of
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… more... download 8kb .zip
Last Modified: August 13, 2014
Christian, W. (2013). Molecular Dynamics Replicated Data Model (Version 1.0) [Computer software]. Retrieved February 1, 2015, from http://www.compadre.org/Repository/document/ServeFile.cfm?ID=12987&DocID=3559
%0 Computer Program %A Christian, Wolfgang %D August 30, 2013 %T Molecular Dynamics Replicated Data Model %7 1.0 %8 August 30, 2013 %U http://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.