OpenMM Workflow

OpenMM is a high-performance toolkit for molecular simulation. MolSysMT provides two-way interoperability with OpenMM, allowing users to build and parameterize systems, run energy minimizations and MD simulations, and seamlessly retrieve coordinates and thermodynamic properties for downstream analysis.

Building the Molecular System

We start by constructing an alanine dipeptide (AceAlaNme) with MolSysMT:

import molsysmt as msm
from molsysmt import pyunitwizard as puw

molsys = msm.build.build_peptide('AceAlaNme')
msm.info(molsys)

form	n_atoms	n_groups	n_components	n_chains	n_molecules	n_entities	n_peptides	n_structures
molsysmt.MolSys	22	3	1	1	1	1	1	1

Interoperability and Conversions

MolSysMT can convert native systems directly into OpenMM objects, including openmm.Topology and fully configured openmm.app.Simulation instances:

omm_topology = msm.convert(molsys, to_form='openmm.Topology')
print(omm_topology)

<Topology; 1 chains, 3 residues, 22 atoms, 21 bonds>

simulation = msm.convert(molsys, to_form='openmm.Simulation', forcefield='AMBER14')
print(simulation)

<openmm.app.simulation.Simulation object at 0x75167c0ae7b0>

Energy Minimization

We query the potential energy of the initial conformation and minimize it with OpenMM:

e_initial = msm.molecular_mechanics.get_potential_energy(simulation)
print(f"Initial potential energy: {e_initial}")

simulation.minimizeEnergy(maxIterations=100)

e_min = msm.molecular_mechanics.get_potential_energy(simulation)
print(f"Minimized potential energy: {e_min}")

Initial potential energy: -55.7942228620533 kilojoule / mole
Minimized potential energy: -86.12218322364657 kilojoule / mole

Molecular Dynamics Simulation

We can integrate equations of motion directly through the OpenMM simulation object:

simulation.step(500)
e_final = msm.molecular_mechanics.get_potential_energy(simulation)
print(f"Potential energy after 500 MD steps: {e_final}")

Potential energy after 500 MD steps: -86.87117403639718 kilojoule / mole

Extracting Simulation States

We retrieve the updated coordinates from OpenMM and store them back into our MolSysMT system:

coords_simulated = msm.get(simulation.context, coordinates=True)
msm.set(molsys, coordinates=coords_simulated)
print(f"Updated MolSys coordinates shape: {msm.get(molsys, coordinates=True).shape}")

Updated MolSys coordinates shape: (1, 22, 3)

Interactive Visualization

We visualize the simulated conformation in 3D using MolSysViewer:

msm.view(molsys)