Grid Services for Parallel Molecular Dynamics with NAMD and CHARMM

Abstract

High-end computing facilities are key to enabling molecular dynamics simulation of biological relevant systems for a sufficiently long simulation period. On the one hand, the trajectory production necessitates a high-performance parallel computer architecture. On the other hand, hundreds of jobs, both trajectory production and analysis, have to be supervised and started more or less automatically. Although high performance computers are now available to a broad scientific community, users are often forced to cope with many low-level details when using these machines for scientific investigations. Grid computing technologies promise to provide seamless access to parallel computers through the abstraction of services hiding the details of the underlying software and hardware infrastructure. In this article, we describe the provision of Grid services for parallel molecular dynamics simulations based on NAMD and CHARMM within the Vienna Grid Environment.KeywordsNAMDCHARMMGrid servicemolecular dynamicsionic liquid