OpenMM PyTorch Plugin

This is a plugin for OpenMM that allows PyTorch static computation graphs to be used for defining an OpenMM TorchForce object, an OpenMM Force class that computes a contribution to the potential energy or used as a collective variable via CustomCVForce.

To use it, you create a PyTorch model that takes a (nparticles,3) tensor of particle positions (in nanometers) as input and produces energy (in kJ/mol) or the value of the collective variable as output.
The TorchForce provided by this plugin can then use the model to compute energy contributions or apply forces to particles during a simulation. TorchForce also supports the use of global context parameters that can be fed to the model and changed dynamically during runtime.

Installation

Installing with conda

We provide conda packages for Linux and MacOS via conda-forge, which can be installed from the conda-forge channel:

conda install -c conda-forge openmm-torch

If you don't have conda available, we recommend installing Miniconda for Python 3 to provide the conda package manager.

Building from source

This plugin uses CMake as its build system.
Before compiling you must install LibTorch, which is the PyTorch C++ API, by following the instructions at https://pytorch.org. You can then follow these steps:

1. Create a directory in which to build the plugin.

2. Run the CMake GUI or ccmake, specifying your new directory as the build directory and the top level directory of this project as the source directory.

3. Press "Configure". (Do not worry if it produces an error message about not being able to find PyTorch.)

4. Set OPENMM_DIR to point to the directory where OpenMM is installed. This is needed to locate the OpenMM header files and libraries. If you are unsure of what directory this is, the following script will print it out.

from simtk import openmm
import os
print(os.path.dirname(openmm.version.openmm_library_path))

5. Set PYTORCH_DIR to point to the directory where you installed the LibTorch.

6. Set CMAKE_INSTALL_PREFIX to the directory where the plugin should be installed. Usually, this will be the same as OPENMM_DIR, so the plugin will be added to your OpenMM installation.

7. If you plan to build the OpenCL platform, make sure that OPENCL_INCLUDE_DIR and OPENCL_LIBRARY are set correctly, and that NN_BUILD_OPENCL_LIB is selected.

8. If you plan to build the CUDA platform, make sure that CUDA_TOOLKIT_ROOT_DIR is set correctly and that NN_BUILD_CUDA_LIB is selected.

9. Press "Configure" again if necessary, then press "Generate".

10. Use the build system you selected to build and install the plugin. For example, if you selected Unix Makefiles, type make install to install the plugin, and make PythonInstall to install the Python wrapper.

Using the OpenMM PyTorch plugin

Tutorials

• A simple simulation of alanine dipeptide with ANI-2x using OpenMM-Torch and NNPOps

Exporting a PyTorch model for use in OpenMM

The first step is to create a PyTorch model defining the calculation to perform.
It should take particle positions in nanometers (in the form of a torch.Tensor of shape (nparticles,3) as input, and return the potential energy in kJ/mol as a torch.Scalar as output.

The model must then be converted to a TorchScript module and saved to a file.
Converting to TorchScript can usually be done with a single call to torch.jit.script() or torch.jit.trace(), although more complicated models can sometimes require extra steps.
See the PyTorch documentation for details.

Here is a simple Python example that does this for a very simple potential---a harmonic force attracting every particle to the origin:

import torch

class ForceModule(torch.nn.Module):
    """A central harmonic potential as a static compute graph"""
    def forward(self, positions):
        """The forward method returns the energy computed from positions.

        Parameters
        ----------
        positions : torch.Tensor with shape (nparticles,3)
           positions[i,k] is the position (in nanometers) of spatial dimension k of particle i

        Returns
        -------
        potential : torch.Scalar
           The potential energy (in kJ/mol)
        """
        return torch.sum(positions**2)

# Render the compute graph to a TorchScript module
module = torch.jit.script(ForceModule())

# Serialize the compute graph to a file
module.save('model.pt')

To use the exported model in a simulation, create a TorchForce object and add it to your System.
The constructor takes the path to the saved model as an argument.
For example,

# Create the TorchForce from the serialized compute graph
from openmmtorch import TorchForce
torch_force = TorchForce('model.pt')

# Add the TorchForce to your System
system.addForce(torch_force)

Defining a model that uses periodic boundary conditions

When defining the model to perform a calculation, you may want to apply periodic boundary conditions.

To do this, call setUsesPeriodicBoundaryConditions(True) on the TorchForce.
The graph is then expected to take a second input, which contains the current periodic box vectors.
You can make use of them in whatever way you want for computing the force.
For example, the following code applies periodic boundary conditions to each particle position to translate all of them into a single periodic cell:

class ForceModule(torch.nn.Module):
    """A central harmonic force with periodic boundary conditions"""
    def forward(self, positions, boxvectors):
        """The forward method returns the energy computed from positions.

        Parameters
        ----------
        positions : torch.Tensor with shape (nparticles,3)
           positions[i,k] is the position (in nanometers) of spatial dimension k of particle i
        boxvectors : torch.tensor with shape (3,3)
           boxvectors[i,k] is the box vector component k (in nanometers) of box vector i

        Returns
        -------
        potential : torch.Scalar
           The potential energy (in kJ/mol)
        """
        # Image articles in rectilinear box
        # NOTE: This will not work for non-orthogonal boxes
        boxsize = boxvectors.diag()
        periodicPositions = positions - torch.floor(positions/boxsize)*boxsize
        # Compute central harmonic potential
        return torch.sum(periodicPositions**2)

Note that this code assumes a rectangular box. Applying periodic boundary conditions with a triclinic box requires a slightly more complicated calculation.

Defining global parameters that can be modified within the Context

The graph can also take arbitrary scalar arguments that are passed in at runtime. For example, this model multiplies the energy by scale, which is passed as an argument to forward().

class ForceModule(torch.nn.Module):
    """A central harmonic force with a user-defined global scale parameter"""
    def forward(self, positions, scale):
        """The forward method returns the energy computed from positions.

        Parameters
        ----------
        positions : torch.Tensor with shape (nparticles,3)
           positions[i,k] is the position (in nanometers) of spatial dimension k of particle i
        scale : torch.Scalar
           A scalar tensor defined by 'TorchForce.addGlobalParameter'.
           Here, it scales the contribution to the potential.
           Note that parameters are passed in the order defined by `TorchForce.addGlobalParameter`, not by name.

        Returns
        -------
        potential : torch.Scalar
           The potential energy (in kJ/mol)
        """
        return scale*torch.sum(positions**2)

When you create the TorchForce, call addGlobalParameter() once for each extra argument.

torch_force.addGlobalParameter('scale', 2.0)

This specifies the name of the parameter and its initial value. The name does not need to match the argument to forward(). All global parameters are simply passed to the model in the order you define them. The advantage of using global parameters is that you can change their values at any time by calling setParameter() on the Context.

context.setParameter('scale', 5.0)

Computing forces in the model

In the examples above, the PyTorch model computes the potential energy. Backpropagation can be used to compute the corresponding forces. That always works, but sometimes you may have a more efficient way to compute the forces than the generic backpropagation algorithm. In that case, you can have the model directly compute forces as well as energy, returning both of them in a tuple. Remember that the force is the negative gradient of the energy.

import torch

class ForceModule(torch.nn.Module):
    """A central harmonic potential that computes both energy and forces."""
    def forward(self, positions):
        """The forward method returns the energy and forces computed from positions.

        Parameters
        ----------
        positions : torch.Tensor with shape (nparticles,3)
           positions[i,k] is the position (in nanometers) of spatial dimension k of particle i

        Returns
        -------
        potential : torch.Scalar
           The potential energy (in kJ/mol)
        forces : torch.Tensor with shape (nparticles,3)
           The force (in kJ/mol/nm) on each particle
        """
        return (torch.sum(positions**2), -2*positions)

When you create the TorchForce, call setOutputsForces() to tell it to expect the model to return forces.

torch_force.setOutputsForces(True)

License

This is part of the OpenMM molecular simulation toolkit originating from Simbios, the NIH National Center for Physics-Based Simulation of Biological Structures at Stanford, funded under the NIH Roadmap for Medical Research, grant U54 GM072970. See https://simtk.org.

Portions copyright (c) 2018-2020 Stanford University and the Authors.

Authors: Peter Eastman

Contributors: Raimondas Galvelis, Jaime Rodriguez-Guerra, Yaoyi Chen, John D. Chodera

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, CONTRIBUTORS 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.