OpenMM

MolSysMT can build an openmm.app.Simulation directly from a molecular system that contains both topology and coordinates. The conversion builds an OpenMM System, creates a Langevin integrator, and initializes the resulting Context with the first requested structure.

import molsysmt as msm

molecular_system = msm.convert(
    msm.systems["alanine dipeptide"]["alanine_dipeptide.h5msm"],
    to_form="molsysmt.MolSys",
)
simulation = msm.convert(
    molecular_system,
    to_form="openmm.Simulation",
    structure_indices=0,
    temperature="300 K",
)

The default platform is CPU, which makes the conversion portable on machines without an accelerator. Request an installed accelerator explicitly, for example with platform="CUDA".

The initial structure is never invented. A source without coordinates is rejected, and when structure_indices contains multiple entries, their order is preserved and the first requested structure initializes the context. An openmm.System alone cannot be converted into a Simulation, because it does not contain the required topology or coordinates. An openmm.Topology can be used when coordinates are supplied explicitly.

Force fields and water models use MolSysMT’s canonical names, such as forcefield="AMBER14" and water_model="TIP3P-FB".

• Custom External Forces
  • Add allowed plane region
  • Add allowed z region
  • Add constant force
  • Add forbidden plane region
  • Add forbidden z region
  • Add point harmonic restraint
  • Add plane harmonic restraint
  • Pin atoms
• Reporters