Backed by researchers and developers from Stanford University, MSKCC, and others around the world.
Want a custom force between two atoms? No problem. Write your force expressions in string format, and OpenMM will generate blazing fast code to do just that. No more hand-writing GPU kernels.
OpenMM is optimized for the latest generation of compute hardware, including AMD (via OpenCL) and NVIDIA (via CUDA) GPUs. We also heavily optimize for CPUs using intrinsics.
We strive to make our binaries as portable as possible. We've tested OpenMM on many flavors of Linux, OS X, and even Windows.
from simtk.openmm.app import * from simtk.openmm import * from simtk.unit import * from sys import stdout pdb = PDBFile('input.pdb') forcefield = ForceField('amber99sb.xml', 'tip3p.xml') system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME, nonbondedCutoff=1*nanometer, constraints=HBonds) integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds) simulation = Simulation(pdb.topology, system, integrator) simulation.context.setPositions(pdb.positions) simulation.minimizeEnergy() simulation.reporters.append(PDBReporter('output.pdb', 1000)) simulation.reporters.append(StateDataReporter(stdout, 1000, step=True, potentialEnergy=True, temperature=True)) simulation.step(10000)
If you publish papers using OpenMM, we kindly ask you cite the following to help feed hungry grad students:P. Eastman, M. S. Friedrichs, J. D. Chodera, R. J. Radmer, C. M. Bruns, J. P. Ku, K. A. Beauchamp, T. J. Lane, L.-P. Wang, D. Shukla, T. Tye, M. Houston, T. Stich, C. Klein, M. R. Shirts, and V. S. Pande. "OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation." J. Chem. Theor. Comput. 9(1):461-469. (2013)
Trusted and used by scientists around the world.
Performance measured in ns/day. Details.
|Simulation Type||CUDA (Titan X Pascal)||OpenCL (Titan X Pascal)||CPU (Xeon E5-2697 v4)|
|Implicit, 2 fs||863||665||19.8|
|Implicit, 5 fs HMR||1386||816||44.1|
|Explicit-RF, 2 fs||607||486||21.0|
|Explicit-RF, 5 fs HMR||1047||689||43.6|
|Explicit-PME, 2 fs||384||288||15.6|
|Explicit-PME, 5 fs HMR||762||430||34.8|
Maintained by the OpenMM team. Copyright 2017, Stanford University