A coarse-grain model is one where some of the fine details of the modelled system has been smoothed over, grouped together, or averaged out. In molecular dynamics, ‘coarse-grain’, as opposed to ‘atomistic’, is a model where all atoms are not represented, but some atoms are grouped together to form a (larger) particle. To justify, the atoms grouped together within the larger particle may have behaviours that are too detailed and of no interest to the present investigation. Such grouping therefore saves computational time, so that longer-timescale ‘interesting’ events can be more readily observed. An early example of coarse-grain MD is the ‘united-atom’ forcefields, where non-ionizable hydrogen atoms are ‘united’ with the heavy atom they bond to. Recent examples include lipid and biomolecular simulations, where the nanosecond time-scale afforded by atomistic MD has been surpassed by microsecond-scale coarse-grain MD simulations.
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.