A method to simulate of molecules in which atoms (or particles in general) within molecules interact under laws of physics (traditionally the classical Newtonian laws) for some time, giving a view of the motion of the molecule. The underlying framework of physical (Newtonian) laws is called ‘molecular mechanics’ (MM). This simulation can be constructed using real ‘balls’ (spheres representing the atoms/particles) and appropriate ‘springs’ (possibly non-Hookean, to represent the interactions between the particles); but more conveniently, it is commonly done in silico, using a model of the molecules in the computer to progress through time according to the physical laws. Though usually only the classical interactions are considered, it is possible to mix in quantum mechanics considerations for certain areas where bond-breaking and bond-forming activities are of interest. This mixed method is called ‘quantum mechanics-molecular mechanics’ (QM/MM).
Published in Chapter:
BioSimGrid Biomolecular Simulation Database
Kaihsu Tai (University of Oxford, UK) and Mark Sansom (University of Oxford, UK)
Copyright: © 2009
|Pages: 20
DOI: 10.4018/978-1-60566-374-6.ch016
Abstract
BioSimGrid is a distributed biomolecular simulation database. It is a general-purpose database for trajectories from molecular dynamics simulations. Though initially designed as a distributed data grid, BioSimGrid allows for installation as a stand-alone instance. This can later be integrated into a wider, networked system. This presentation of BioSimGrid follows a scenario in biological research to demonstrate how to install the system, and how to deposit, query, and analyze trajectories in this system, with real Python code examples for each step. What then follow are explanations of the underlying concepts in the implementation of BioSimGrid: relational database, distributed computing, and the input/output (deposit and analysis) modules. Finishing the presentation is a discussion of the emerging trends and concerns in the further development of BioSimGrid and similar biological databases. This discussion touches on quality-assurance issues and the use of BioSimGrid as a back-end for other speciality databases. The experience of developing BioSimGrid compels the conclusion: In the development and maintenance of biomolecular simulation databases, it is essential that sustainability be asserted as a key principle.