GneimoSim: A modular internal coordinates molecular dynamics simulation package

• Published in: Journal of computational chemistry 2014-12, Vol.35 (31), p.2245-2255
• Main Authors: Larsen, Adrien B., Wagner, Jeffrey R., Kandel, Saugat, Salomon-Ferrer, Romelia, Vaidehi, Nagarajan, Jain, Abhinandan
• Format: Article
• Language: English
• Subjects: Eulers equations; GNEIMO; GneimoSim; ICMD; Models, Molecular; molecular dynamics; Molecular Dynamics Simulation; Molecules; Proteins; Proteins - chemistry; refinement; Sampling; Simulation; Software; torsional MD
• ISSN: 0192-8651; 1096-987X
• DOI: 10.1002/jcc.23743

The generalized Newton–Euler inverse mass operator (GNEIMO) method is an advanced method for internal coordinates molecular dynamics (ICMD). GNEIMO includes several theoretical and algorithmic advancements that address longstanding challenges with ICMD simulations. In this article, we describe the GneimoSim ICMD software package that implements the GNEIMO method. We believe that GneimoSim is the first software package to include advanced features such as the equipartition principle derived for internal coordinates, and a method for including the Fixman potential to eliminate systematic statistical biases introduced by the use of hard constraints. Moreover, by design, GneimoSim is extensible and can be easily interfaced with third party force field packages for ICMD simulations. Currently, GneimoSim includes interfaces to LAMMPS, OpenMM, and Rosetta force field calculation packages. The availability of a comprehensive Python interface to the underlying C++ classes and their methods provides a powerful and versatile mechanism for users to develop simulation scripts to configure the simulation and control the simulation flow. GneimoSim has been used extensively for studying the dynamics of protein structures, refinement of protein homology models, and for simulating large scale protein conformational changes with enhanced sampling methods. GneimoSim is not limited to proteins and can also be used for the simulation of polymeric materials. This paper describes the modular architecture of the GneimoSim software package for performing long time scale internal coordinate molecular dynamics simulations. GneimoSim includes advanced dynamics methods, integrators for robust long time scale dynamics, interfaces for all‐atom forcefields such as AMBER and CHARMM, and the Generalized Born solvation model. The software is available at no cost for academic use.