Biomolecular simulation is the application of molecular dynamics simulations to biochemical research questions. Processes that can be modeled include, but are not limited to, protein folding, drug binding, membrane transport, and the conformational changes critical to protein function.
While biomolecular simulation could be considered a sub-field of computational chemistry, it is sufficiently specialized that Compute Canada has a Biomolecular Simulations National Team that supports this area. There is nevertheless some overlap of software tools between the two fields. See Computational chemistry for an annotated list of available software packages in that area.
The following software packages are available on Compute Canada's HPC resources:
- OpenKIM, the Knowledgebase of Interatomic Models
- PLUMED, a library for code development related to the calculation of free energy in molecular dynamics simulations. See also GROMACS.
Python Packages (Python Wheels)
This list contains a selection of useful wheels, but is not to be considered complete:
- MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats.
- MDTraj can also read, write and analyze MD trajectories with only a few lines of Python code with wide MD format support.
- Biopython is a set of freely available tools for biological computation.
- foyer is a package for atom-typing as well as applying and disseminating force fields.
- mBuild is a hierarchical, component based molecule builder.
- mdsynthesis is a persistence engine for molecular dynamics data.
- nglview: NGL Viewer is a collection of tools for web-based molecular graphics.
- ParmEd is a general tool for aiding in investigations of biomolecular systems using popular molecular simulation packages.
- PyRETIS is a Python library for rare event molecular simulations with emphasis on methods based on transition interface sampling and replica exchange transition interface sampling.
If you require additional Python packages or newer versions, please contact Support.
We are working on providing practical examples on how to do Benchmarking of MD-Simulations. Please stay tuned.
- Ron O. Dror, Robert M. Dirks, J.P. Grossman, Huafeng Xu, and David E. Shaw. "Biomolecular Simulation: A Computational Microscope for Molecular Biology." Annual Review of Biophysics, 41:429-452, 2012. https://doi.org/10.1146/annurev-biophys-042910-155245