OpenMM Continuity Force

This is a plugin for OpenMM that implements a custom many-particle force called a "ContinuityForce". This force aims to ensure that all particles in a set remain continuously connected in space. More precisely, if we imagine the particles as nodes of a network and draw an edge between particles that are closer than a cutoff distance (d), then the nodes would all be in the same component of the network. In other words, there exists a path of some length between any two nodes i and j.

ContinuityForce achieves this by classifying particles into components on the fly and adding an attractive force between pairs of particles belonging to different components. The particles are chosen each dynamics step as the closest possible pairs between the two components. The attractive force is of the form E(r)=k*(r-d)², where r is the separation between the particles and d is a user-defined cutoff distance.

This was originally designed to aid FlexibleTopology simulations (preprint). This plugin was made using the "OpenMMExamplePlugin" template.

Preparing the Environment

I recommend using a CONDA environment for easy installation. Before installing this plugin, you should create this environment and install the openmm and swig packages:

conda install -c conda-forge openmm
conda install swig

If you need to install cmake this can also be done using CONDA:

conda install cmake

Building/Installing The Plugin

To build and install openmmcontinuityforce, follow these steps:

1. Clone this repository to your own machine.

2. Create a directory in which to build the plugin. I suggest openmmcontinuityforce/build.

3. Change to the build directory, and run cmake: cmake .. and open ccmake: ccmake ..

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 using CONDA, this directory will be something like: /your/path/to/conda/pkgs/openmm-7.7.0-py39h9717219_0. NOTE: this is the pkgs directory and not the envs directory!

Your particular version and build of OpenMM installed in this environment can be found by running conda list | grep openmm.

5. Set CMAKE_INSTALL_PREFIX to the directory where the plugin should be installed. I suggest making this the same as OPENMM_DIR, so the plugin will be added to your OpenMM installation.

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

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

8. Type make install, followed by make PythonInstall.

Test Cases

To run all the test cases build the "test" target by typing make test.

Accessing ContinuityForce in Python

There are different ways to make the plugin accessible in a python script. I recommend including the following line in your python script:

omm.Platform.loadPluginsFromDirectory('/path/to/your/anaconda/pkgs/openmm-7.7.0-py39h9717219_0/lib/plugins')

where again you will likely need to change the version and build of OpenMM to match that on your machine.

You can then use the plugin in your Python scripts:

from openmmcontinuityforce import ContinuityForce
force = ContinuityForce()