Technical Paper

On the Development of Molecula Numerica: A Real-Time Visual Molecular Dynamics Simulator

Hiroshi ABEa* and Umpei NAGASHIMAb

aThree Wells
874-3 Kamiarai, Tokorozawa, Saitama, 359-1142, Japan
bResearch Institute for Computational Science ( RICS )
National Institute of Advanced Industrial Science and Technology ( AIST ), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan.

(Received: September 16, 2008; Accepted for publication: December 4, 2008; Advance publication: February 2, 2009)

A real-time visual molecular dynamics simulator, Molecula Numerica is developed. The simulator is designed with modern object-oriented and template meta-programming techniques and is developed with C++. The software is supposed to run most effectively on typical high-end personal computers, which are expected to have multi-cored CPU with SIMD co-processors, and to have a high-end graphic board with high speed BUS. The software adopts multi-platform GUI library and standard libraries so as to be able to run on popular operating systems such as Microsoft Windows, MacOS X or the others. The software can deal with both single-site atoms and multi-site molecules. The multi-site molecules are dealt with as a rigid model. The governing equation of rotational motion of rigid molecules is the quaternion-based equation. The atoms/molecules are defined as C++ Classes. The force calculations between any two of the Classes are defined separated from their class definition using double dispatch mechanism of C++. The mechanism reduces the code-maintenance cost yielded by adding new force models. As an example of simulation, a scene of dissolving salts into water is shown. The executables of the software are available free of charge for MacOS X and for MS Windows.

Keywords: MD, Rigid water model, Quaternion, Object-oriented, Template programming, C++


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