Optimization of the Amber Force Field for Nucleic Acid Bases

Victor Anisimov, Individual Award/Unaffiliated

Usage Details

Classical molecular dynamics is a ubiquitous tool in bio-pharmaceutical, chemical, and material sciences. Thousands of research teams Nationwide and across the Globe depend on the Amber force field to conduct computer simulations of important practical applications. Developed in 1994, the Amber force field for DNA bases has not been revised since. The present project updates the Amber force field by employing an enhanced experiment-derived training data set and a novel protocol to reliably identify a stable minimum in the parameter space to reproduce a wide array of target data.

The present work employs unique capabilities of Blue Waters that enable thousand-node scale quantum mechanics jobs and massive parallel arrays of molecular dynamics simulations. Large number of compute nodes and backfill opportunity make Blue Waters an ideal resource for this project. Parameter optimization drastically improves the accuracy of computer simulation, and creates the lasting effect reaching out to many science disciplines.