Introduction

The Molecular Integration Simulation Toolkit (MIST) started development as part of the ExTASY (Extensible Tools for Advanced Sampling and analYsis) project and has been mainly written by Iain Bethune.

In order for new integration algorithms to be widely adopted by the biomolecular simulation community, their effectiveness must be demonstrated on systems of biological relevance. Typically, integrator development is carried out within simplified MD codes, which lack the efficient force evaluation and paralellisation approaches available in 'production' MD codes such as GROMACS, NAMD and LAMMPS, which have large existing user bases. The excellent performance and scalability of these codes comes at a cost of software complexity, and thus there is a barrier to the implementation of new algorithms, their testing at scale, and their eventual adoption by the wider community.

MIST overcomes this barrier by providing two things:

1. a simple API for integrator developers which hides the complexities of real MD codes, enabling rapid development of new integration algorithms at a higher level of abstraction; and
2. a plug-in interface, enabling the new integrators to be deployed directly in several MD codes, taking advantage of their highly efficient force evaluation code, file format support, and supporting tool chains.

Contents

• About
• Installing MIST
• Running LAMMPS with MIST
• Running GROMACS with MIST
• Running Amber with MIST
• Running NAMD-Lite with MIST
• MIST Integrators
• Constraints with MIST
• Adding new integrators into the MIST library
• Testing MIST
• Publications