1. Introduction

OpenMM consists of two parts:

1. A set of libraries that lets programmers easily add molecular simulation features to their programs
2. An “application layer” that exposes those features to end users who just want to run simulations

This guide is divided into three sections:

• Part I (Chapters 2-7) describes the application layer. It is relevant to all users, but especially relevant to people who want to use OpenMM as a stand-alone application for running simulations.
• Part II (Chapters 8-17) describes how to use the OpenMM libraries within your own applications. It is primarily relevant to programmers who want to write simulation applications.
• Part III (Chapters 18-22) describes the mathematical theory behind the features found in OpenMM. It is relevant to all users.

1.1. Online Resources

You can find more documentation and other material at our website http://simtk.org/home/openmm. Among other things there is a discussion forum, a wiki, and videos of lectures on using OpenMM.

1.2. Referencing OpenMM

Any work that uses OpenMM should cite the following publication:

P. Eastman, M. S. Friedrichs, J. D. Chodera, R. J. Radmer, C. M. Bruns, J. P. Ku, K. A. Beauchamp, T. J. Lane, L.-P. Wang, D. Shukla, T. Tye, M. Houston, T. Stich, C. Klein, M. R. Shirts, and V. S. Pande. “OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation.” J. Chem. Theor. Comput. 9(1): 461-469. (2013).

We depend on academic research grants to fund the OpenMM development efforts; citations of our publication will help demonstrate the value of OpenMM.

1.3. Acknowledgments

OpenMM software and all related activities, such as this manual, are funded by the Simbios National Center for Biomedical Computing through the National Institutes of Health Roadmap for Medical Research, Grant U54 GM072970. Information on the National Centers can be found at http://nihroadmap.nih.gov/bioinformatics.