Molecular dynamics in a grid computing environment: experiences using DL_POLY_3 within the eMinerals escience project

Abstract

We use the example of a study of the compressibility anomaly in amorphous silica to illustrate how molecular-scale simulations can be performed using grid computing. The potential for running many simulations within a single study requires the use of new data management methods, which are discussed in this paper. The example of silica highlights the advantages of the use of grid computing for studying subtle effects.

Keywords:

• Amorphous silica
• Grid computing
• DL_POLY_3
• XML
• Chemical markup language
• eMinerals

Acknowledgements

We acknowledge financial support from NERC for the eMinerals project.

Notes

It should be noted that for our sample sizes, DL_POLY_2 is better optimised than DL_POLY_3, but as our development code, only DL_POLY_3 contains the capabilities described in Section 4.2.