BioSimSpace.MD

This package provides functionality for configuring and running a variety of molecular dynamics simulation processes.

At present, we provide support for finding molecular dynamics packages and automatically configuring and starting processes for the user. BioSimSpace.MD acts as a wrapper around BioSimSpace.Process, meaning that the user doesn’t need to specify the molecular dynamics package that they wish to use. This will automatically be determined from the file format of the molecular configuration, the type of simulation protocol that was chosen, and the hardware resources that are available.

As an example:

import BioSimSpace as BSS

# Read a molecular system from file.
system = BSS.IO.readMolecules(["ala.crd", "ala.top"])

# Create a default minimisation protocol.
protocol = BSS.Protocol.Minimisation()

# Automatically find an appropriate molecular dynamics package on the host environment,
# set up the simulation and return a running process. Since the system was generated from 
# a CRD and TOP file, BSS.MD will try to find an AMBER package.
process = BSS.MD.run(system, protocol)