The mm Module¶

Introduction¶

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 Topology describing how the particles of an EntityHandle interact. The Simulation class connects the EntityHandle with a Topology and allows you to perform energy minimizations or move the simulation through time using an Integrator. A Topology can either be built from scratch by adding one interaction after the other or automatically using the TopologyCreator. The process of Topology building and setting up a Simulation gets controlled with the Settings.

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)

Installation¶

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.:

cmake . -DENABLE_MM=1 -DOPEN_MM_INCLUDE_DIR=/path/to/openmm/include
        -DOPEN_MM_LIBRARY=/path/to/openmm/lib/libOpenMM.so
        -DOPEN_MM_PLUGIN_DIR=/path/to/openmm/lib/plugins

Setting up a simple simulation¶

from ost.mol import mm

prot=io.LoadPDB('1crn',remote=True)

#set up the simulation
settings = mm.Settings()
settings.integrator = mm.LangevinIntegrator(310,1,0.002)
settings.forcefield = mm.LoadCHARMMForcefield()
sim = mm.Simulation(prot,settings)

#minimize it
sim.ApplySD(tolerance = 1.0, max_iterations = 200)

#create a trajectory observer and register it to the simulation
#every 10 steps, the actual positions will be written down to disk
observer = mm.TrajWriter(10,"example_traj.pdb","example_traj.dcd")
sim.Register(observer)

#run the simulation
sim.Steps(10000)

#Trajectory Observer needs to finalize, otherwise you might get a corrupt dcd file
observer.Finalize()

Doing more sophisticated stuff¶

You want to create your own BuildingBlock to parameterize custom residues? Or even generate your own custom Forcefield? Check out the mm dir in the examples/code_fragments directory.

Documentation¶