An Open Environment for Automation of Molecular Dynamics Simulations of Membrane-Active Host Defense Peptides
College: Liberal Arts and Sciences
Award year: 2014-2015
Molecular dynamics methods changed the way chemists and biologists approach the computational material design problems. Due to complexity of connecting the macroscopic phenomena with atomistic processes, conducting research involving molecular dynamics simulations is an extremely labor-intensive work. Many factors—such as the need to tailor job scripts to specific computational systems, difficulty in tracking projects distributed across several systems, writing scripts over and over for each new science problem, and more—make conducting computational biophysics simulations on high-performance computing (HPC) resources labor-intensive. This forces researchers to spend valuable time on conducting the simulations, rather than focusing on the science problem. The goal of this project is to develop the architecture design for an extensible software package, the Computational Discovery Desktop (CDD), that will provide a customizable human-HPC interface to conduct computational projects in a manner requiring minimal user intervention, encouraging the reuse of plug-in components, and providing management of computational projects. The long-term goal of the project is enhancing the efficiency of interaction of the broad science and engineering community.