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, J. Swails, J. D. Chodera, R. T. McGibbon, Y. Zhao, K. A. Beauchamp, L.-P. Wang, A. C. Simmonett, M. P. Harrigan, C. D. Stern, R. P. Wiewiora, B. R. Brooks, and V. S. Pande. “OpenMM 7: Rapid development of high performance algorithms for molecular dynamics.” PLOS Comp. Biol. 13(7): e1005659. (2017)
Installation¶
If you are compiling OpenStructure from source, you need to specifically enable
support for OpenMM. You do this by enabling the
ENABLE_MM flag and setting the OPEN_MM_INCLUDE_DIR, OPEN_MM_LIBRARY
and OPEN_MM_PLUGIN_DIR flags when calling cmake. See
here for details and examples.
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.