The results of the molecular dynamics simulation is called a trajectory. This is a time-series of molecular conformations, or in other words, a movie of three-dimensional snapshots for the molecules in the system. For a system of N particles and m frames, a trajectory can be seen conceptually as a 3N × m matrix: On one side, it contains the 3N Cartesian coordinates, three scalars for each atom. On the other, it contains a list of frames each associated with a time-point. Often the time-step for Newtonian integration for an atomistic simulation is 1 fs or 2 fs, and the snapshots are recorded at the rate of 1 ps per frame. For a 1 ns trajectory, this gives 106 time-steps and 103 frames.
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.