Relaxed Complex Method
NAMD
Amber
Gromos
Gromacs
Virtual Screening
AutoDock
MGLTools
Resources
The RC/MD workflow is complex and computationally demanding, but with strong potentials for application to other infectious diseases. While the MD simulations are more scalable in a high performance computing cluster with low latency network, the virtual screening process requires little interprocessor communication and is highly suitable for a distributed grid environment. The Avian Flu Grid is an integrative effort based on the technology developed by several member institutes to support advanced scientific research for avian flu.
The calculations based on these state-of-the-art computational approaches is managed by the CSF4 meta-scheduler (http://gcsf.sourceforge.net) through either a portal environment (https://portal.pragma-grid.net:9443) or Opal-based application specific web services (http://nbcr.net/serivces) which leverages CSF4 for job distribution.
Long running MD simulations with a large number of processors are done using TeraGrid (http://www.teragrid.org) resources, and HPC resources available at the National Biomedical Computation Resource (http://nbcr.net), and Maui High Performance Computing Center (http://www.mhpcc.edu). The complex work flows are captured using the Vision workflow management tools (http://mgltools.scripps.edu).
Data
Computational data management and sharing across different sites is simplified using Gfarm (http://datafarm.apgrid.org). The simulation setup, and post-analysis are carried out using M*Grid and Glyco-M*Grid (http://www.mgrid.or.kr/), and virtual screening results are managed using the Scientific Data Grid (http://pragma.sdg.ac.cn/).
In addition, Glyco-M*Grid, a grid portal-based integrated environment for e-Glycomics, provides a powerful tool for tackling the glycobiology in the avian flu systems. Preliminary equilibration and minimization steps of the MD simulations as well as virtual screening experiments are carried using PRAGMA grid. Natural compound library is screened using the NaPIMM portal (http://www.usm.my).