Paper Citing NAMD - Abstract
Shen, Ning; Fan, Ye; Pamidighantam, Sudhakar
E-science infrastructures for molecular modeling and parametrization
JOURNAL OF COMPUTATIONAL SCIENCE, 5:576-589, JUL 2014
E-science infrastructures are becoming the essential tools for computational scientific research. In this paper, we describe two e-science infrastructures: Science and Engineering Applications Grid (SEAGrid) and molecular modeling and parametrization (ParamChem). The SEAGrid is a virtual organization with a diverse set of hardware and software resources and provides services to access such resources in a routine and transparent manner. These essential services include allocations of computational resources, client-side application interfaces, computational job and data management tools, and consulting activities. ParamChem is another e-science project dedicated for molecular force-field parametrization based on both ab-initio and molecular mechanics calculations on high performance computers (HPCs) driven by scientific workflow middleware services. Both the projects share a similar three-tier computational infrastructure that consists of a front-end client, a middleware web services layer, and a remote HPC computational layer. The client is a Java Swing desktop application with components for pre- and post-data processing, communications with middleware server and local data management. The middleware service is based on Axis2 web service and MySQL relational database, which provides functionalities for user authentication and session control, HPC resource information collections, discovery and matching, job information logging and notification. It can also be integrated with scientific workflow to manage computations on HPC resources. The grid credentials for accessing HPCs are delegated through MyProxy infrastructure. Currently SEAGrid has integrated several popular application software suites such as Gaussian for quantum chemistry, NAMD for molecular dynamics and engineering software such as Abacus for mechanical engineering. ParamChem has integrated CGenFF (CHARMM General Force-Field) for molecular force-field parametrization of drug-like molecules. Long-term storage of user data is handled by tertiary data archival mechanisms. SEAGrid science gateway serves more than 500 users while more than 1000 users use ParamChem services such as atom typing and initial force-field parameter guess at present. (C) 2014 Elsevier B.V. All rights reserved.
