You are reading the documentation for version 1.6 of OpenStructure. You may also want to read the documentation for: 1.1 1.2 1.3 1.4 1.5 devel
The mm Module¶
The mol.mm module provides a wrapper around the
OpenMM molecular mechanics library to provide
basic molecular dynamics (MD) capabilities fully embedded into the OpenStructure universe.
The heart of every simulation is the
Latest Publication of OpenMM: 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)
OpenStructure does not come by default with OpenMM support. You have to install it as an additional dependency and recompile OpenStructure to dive into the amazing world of GPU accelerated molecular mechanics. Once installed, you have to pass cmake additional flags to allow compilation with OpenMM support. e.g.:
Setting up a simple simulation¶
Doing more sophisticated stuff¶
This documentation is still under heavy development.
If something is missing or if you need the C++ API description in doxygen style, check our old documentation for further information.
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