OpenMM Molecular Dynamics module
Submodules
Module contents
OpenMM Molecular Dynamics refinement module for HADDOCK3.
The potential of OpenMM can be exploited to perform potentially different tasks, such as:
Run MD simulation for each model from previous step;
Refine the models in the middle of a docking run. For example, it can be used to refine the models coming from a [rigidbody] module before [flexref] is executed, or to replace the [mdref] step.
Generate conformers prior to their use in a thorough docking run.
To get a list of all possible parameters, run:
>>> haddock3-cfg -m openmm
Module workflow:
Generate openmm topology and fix atoms
Build solvation box
Equilibration solvation box restraining the protein
Run MD simulation: increase temperature, run MD, reduce temperature.
Either generate an ensemble of multiple frames or return the last frame.
This module will refine all models coming from the previous workflow step and send them to the next step in the workflow. If you want to use other modules such as flexref or emref after the OpenMM module, you need to recreate the topologies by simply adding a [topoaa] step in the workflow. See examples in examples/thirdparty/openmm folder.
- class haddock.modules.refinement.openmm.HaddockModule(order, path, initial_params=PosixPath('/opt/hostedtoolcache/Python/3.10.15/x64/lib/python3.10/site-packages/haddock/modules/refinement/openmm/defaults.yaml'))[source]
Bases:
BaseHaddockModule
HADDOCK3 OpenMM module.
- classmethod confirm_installation() None [source]
Confirm installation of openmm and pdfixer.
- Raises:
ThirdPartyIntallationError – When OpenMM is not installed
ThirdPartyIntallationError – When OpenMM pdbfixer is not installed