Abstract We present MIST, the Molecular Integration Simulation Toolkit, a lightweight and efficient software library written in C++ which provides an abstract interface 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, temperature control using Langevin Dynamics, and two tempering schemes. We describe the architecture and functionality of the library and the C and Fortran 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. Program Title: MIST — Molecular Integration Simulation Toolkit Program Files doi: http: dx.doi.org 10.17632 m2v3483r35.1 Licensing provisions: BSD 2-clause Programming language: C++ (C and Fortran interfaces) Nature of problem: Production Molecular Dynamics codes have become increasingly complex, making it difficult to implement new functionality, especially algorithms that modify the core MD integration loop. This places a barrier in the way of new algorithms making their way from theory to implementation. Solution method: MIST provides a simplified abstract interface for integrator developers that may be interfaced via source-code patches and a library API to a variety of MD codes, with minimal loss of performance. Restrictions and unusual features: MIST interfaces only to specific versions of MD codes: Amber 14, Gromacs 5.0.2 and NAMD-Lite 2.0.3 Additional comments: MIST is freely available from https: bitbucket.org extasy-project mist .
OpenMM is a molecular dynamics simulation toolkit with a unique focus on extensibility. It allows users to easily add new features, including forces with novel functional forms, new integration algorithms, and new simulation protocols. Those features automatically work on all supported hardware types (including both CPUs and GPUs) and perform well on all of them. In many cases they require minimal coding, just a mathematical description of the desired function. They also require no modification to OpenMM itself and can be distributed independently of OpenMM. This makes it an ideal tool for researchers developing new simulation methods, and also allows those new methods to be immediately available to the larger community.