MIST: A Simple and Efficient Molecular Dynamics Abstraction Library for Integrator Development

TL;DR

MIST is a lightweight C++ library that abstracts molecular dynamics codes, enabling rapid development of new integrators with minimal overhead across various platforms and MD software.

Contribution

The paper introduces MIST, a portable, efficient toolkit that simplifies the development of new molecular dynamics integrators across multiple simulation packages.

Findings

MIST adds negligible overhead in serial and parallel cases.

Supports integration with NAMD-Lite, GROMACS, and Amber.

Demonstrated use in free energy landscape simulation of Alanine-12.

Abstract

We present MIST, the Molecular Integration Simulation Toolkit, a lightweight and efficient software library written in C++ which provides an abstract in- terface to common molecular dynamics codes, enabling rapid and portable development of new integration schemes for molecular dynamics. The initial release provides plug-in interfaces to NAMD-Lite, GROMACS and Amber, and includes several standard integration schemes, a constraint solver, tem- perature control using Langevin Dynamics, and two tempering schemes. We describe the architecture and functionality of the library and the C and For- tran APIs which can be used to interface additional MD codes to MIST. We show, for a range of test systems, that MIST introduces negligible overheads for serial, shared-memory parallel, and GPU-accelerated cases, except for Amber where the native integrators run directly on the GPU itself. As a demonstration of the capabilities of MIST, we describe a simulated tempering simulation used to study the free energy landscape of Alanine-12 in both vacuum and detailed solvent conditions.