posted on 2024-01-04, 23:05authored bySantiago Antolínez, Peter Eugene Jones, James C. Phillips, Jodi A. Hadden-Perilla
All-atom molecular
dynamics (MD) simulations are an essential structural
biology technique with increasing application to multimillion-atom
systems, including viruses and cellular machinery. Classical MD simulations
rely on parameter sets, such as the AMBER family of force fields (AMBERff),
to accurately describe molecular motion. Here, we present an implementation
of AMBERff for use in NAMD that overcomes previous limitations to
enable high-performance, massively parallel simulations encompassing
up to two billion atoms. Single-point potential energy comparisons
and case studies on model systems demonstrate that the implementation
produces results that are as accurate as running AMBERff in its native
engine.