In this project, the dynamics of rigid bodies in implemented for OpenMM, which is provided with the following new features:
-
A
RigidBodyIntegratorclass for performing a symplectic, time-reversible, and volume-preserving integration of the Hamiltonian equations of motion for a system composed of rigid bodies as well as free atoms. -
An extension of the
ForceFieldclass which enables the definition of rigid-body templates and the creation of systems containing rigid bodies. -
An extension of the
StateDataReporterclass which is able to display the correct temperature (considering the reduced number of degrees of freedom), as well as the translational and rotational parts of the kinetic energy.
This plugin was built upon the official OpenMM Example Plugin.
If you use this plugin, please cite the paper which contains the employed formulation:
- Silveira and Abreu, Journal of Chemical Physics 2017, 147, 124104, doi: 10.1063/1.5003636
In Bibtex format:
@article{Silveira_and_Abreu_2017,
doi = {10.1063/1.5003636},
year = 2017,
publisher = {{AIP} Publishing},
volume = {147},
number = {12},
pages = {124104},
author = {Ana J. Silveira and Charlles R. A. Abreu},
title = {Molecular dynamics with rigid bodies: Alternative formulation and
assessment of its limitations when employed to simulate liquid water},
journal = {The Journal of Chemical Physics}
}
In the following instructions, it is assumed that OpenMM is already installed in your system.
Clone the git repository locally:
git clone https://github.com/craabreu/openmm_rigidbody_plugin.git
You will need CMake to build the plugin. Once it is installed, you can make:
cd openmm_rigidbody_plugin
mkdir build && cd build
cmake ..
make
make install
make PythonInstall
The commands make install and make PythonInstall might require administrator privileges. The
former will install the plugin libraries and the latter will install the python module. In order
to test the installation, please run:
make test
class ForceField(simtk.openmm.app.ForceField):
def registerBodyTemplate(self, name, residue, pattern=None):
"""
Register a new rigid body template.
Parameters
----------
name : string
A name for the rigid body template being registered.
residue : string
The name of the residue template to which this body belongs.
pattern : string, optional, default=None
A string containing a regular expression for selecting the atoms in residue which will
form the body. A list of atom names can be passed as '(name1|name2|...)', for instance.
Only actual atoms will be considered (i.e. virtual sites will be ignored). If patttern
is None, then the whole residue will form the rigid body.
"""
def createSystem(self, topology, **kwargs):
"""
Construct an OpenMM System representing a Topology with this force field. This extends
the original method by creating rigid bodies from previously registered body templates.
Parameters
----------
topology : Topology
The Topology for which to create a System.
kwargs : multiple types
All keyword arguments of the original `ForceField.createSystem` method, plus:
mergeList : list(list(int)), optional, default=None
A nested list of indices of rigid bodies to be merged together after the templates
are applied. If this is None, then no merging will occur.
removeConstraints : bool, optional, default=False
If true, every constraint involving at least one atom that belongs to a rigid body
will be silently removed from the system.
removeForces : bool, optional, default=False
If true, all interactions whose all involved atoms belong to the same rigid body
will be silently removed from the system.
Returns
-------
system : System
The newly created System.
bodyIndices : list(int)
A list containing the index of the rigid body to which every atom belongs (note:
index=0 for free atoms).
"""class RigidBodyIntegrator(simtk.openmm.Integrator):
def __init__(self, stepSize, bodyIndices):
"""
Create a Rigid Body Integrator.
Parameters
----------
stepSize : double
The step size with which to integrate the system (in picoseconds).
bodyIndices : list(int)
A list containing the index of the rigid body to which every atom belongs (note:
index=0 for free atoms).
"""
def setRotationMode(mode):
"""
Defines the mode of rotational move integration.
Parameters
----------
mode : int
The mode of rotation, where mode=0 consisting in using an exact solution for rotations
spanning the whole time step, while mode=n consists in using a NO-SQUISH solution with
the time step split into n small steps.
"""
def step(self, steps):
"""
Advance a simulation through time by taking a series of time steps.
Parameters
----------
steps : int
The number of time steps to be taken.
"""class StateDataReporter(simtk.openmm.app.StateDataReporter):
def __init__(self, *args, **kwargs):
"""
Create a State Data Reporter.
Parameters
----------
args : multiple types
All positional arguments of the original `StateDataReporter` constructor.
kwargs : multiple types
All keyword arguments of the original `StateDataReporter` constructor, plus:
translationalEnergy : bool, optional, default=False
Whether to write the translational part of the kinetic energy to the file.
rotationalEnergy : bool, optional, default=False
Whether to write the rotational part of the kinetic energy to the file.
"""import simtk.openmm as mm
from simtk.openmm import app
import rigidbodyplugin as rbmm
pdb = app.PDBFile('config.pdb')
forcefield = rbmm.ForceField('model.xml')
forcefield.registerBodyTemplate('water', 'HOH')
(system, bodies) = forcefield.createSystem(pdb.topology, nonbondedMethod=app.PME,
removeConstraints=True, removeForces=True)
integrator = rbmm.RigidBodyIntegrator(1.0*unit.femtoseconds, bodies)
integrator.setRotationMode(0)
reporter = rbmm.StateDataReporter(stdout, 1, step=True, temperature=True,
translationalEnergy=True, rotationalEnergy=True)
simulation = app.Simulation(pdb.topology, system, integrator,
platform=mm.Platform.getPlatformByName('CUDA'),
properties={'Precision': 'mixed'})
simulation.context.setPositions(pdb.positions)
simulation.context.setVelocitiesToTemperature(300*unit.kelvin)
simulation.reporters.append(reporter)
simulation.step(1000)In its current version, this plugin can be executed using either the Reference or the CUDA platform of OpenMM. The OpenCL platform is not supported.
MIT License
Copyright (c) 2018, Charlles R. A. Abreu
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.