The MD package provides functionality for automatically configuring and running molecular dynamics simulations. The function will choose the most appropriate molecular dynamics driver based on the software available on the host, the available hardware, the molecular System, and Protocol, returning the user a handle to a Process object to run the simulation.


run(system, protocol[, autostart, name, …]) Auto-configure and run a molecular dynamics process.


import BioSimSpace as BSS

# Load a molecular system from file.
system = BSS.IO.readMolecules(BSS.IO.glob("amber/ala/*")

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

# Find a molecular dynamics package on the host system that supports the
# system and protocol defined above. If a package exists, BioSimSpace
# will auto-generate all of the required input files and return a handle
# to a process that can run the simulation.
process =, protocol)

# Now start the process in the background.