Biomolecular simulation

General

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.

Software Packages

The following software packages are available on Compute Canada's HPC resources:

• AMBER
• GROMACS
• NAMD
• DL_POLY
• LAMMPS
• OpenKIM, the Knowledgebase of Interatomic Models
• OpenMM
• PLUMED, a library for code development related to the calculation of free energy in molecular dynamics simulations. See also GROMACS.
• Rosetta

Benchmarking MD-Simulations

We are working on providing practical examples on how to do Benchmarking of MD-Simulations. Please stay tuned.