A Fast and Parallelized Procedure for Checking Molecular Dynamics 3D Structure

Abstract

ABSTRACT Structures built for or generated from Molecular Dynamics simulations can often have problems such as wrong chiralities, bad parameter assignment, steric clashes, and/or distorted geometries. It is important to be able to detect such problems in a rapid and automated way since such issues can prevent subsequent simulations from running successfully. Here we detail a structure check procedure which focuses on checking for some of the more common structural issues, including atomic overlaps, distorted bonds, and ring intersections, as well as the strategies for parallelizing the check procedure so it can rapidly detect issues in structures with millions of atoms.