OpenMM XTB Plugin

This project provides a connection between OpenMM and XTB. It lets you compute forces and energies with the semi-empirical quantum chemistry methods provided by XTB.

This plugin requires XTB and OpenMM 8.1 or later.

Installation

The easiest way to install this package along with all dependencies is with the conda or mamba package manager.

mamba install -c conda-forge openmm-xtb

Building From Source

This project uses CMake for its build system. To build it, 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".

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 OpenMM was installed with conda, this should be the root directory of the conda environment.

5. Set XTB_INCLUDE_DIR and XTB_LIBRARY_DIR to point to the directories where the XTB header files and libraries are installed.

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

8. 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 Plugin

The plugin can be used in two ways: by directly creating a force and adding it to your System, or by using a ForceField.

Creating a Force Directly

This is the most general and flexible approach, giving complete control over all aspects. For example, you can use XTB to compute forces on some parts of the system but a classical force field to compute the forces on other parts. To use this method, simply create a XtbForce object and add it to your System. For example,

from openmmxtb import XtbForce
system.addForce(XtbForce(XtbForce.GFN2xTB, 0.0, 1, False, particleIndices, atomicNumbers))

The arguments are as follows.

• method: the method to use for computing forces and energy. The currently supported options are GFN1xTB, GFN2xTB, and GFNFF.
• charge: the total charge of the system
• multiplicity: the spin multiplicity
• periodic: whether to apply periodic boundary conditions
• particleIndices: a list containing the indices of the particles within the System to which the force should be applied. This allows you to use XTB for only part of the full system.
• atomicNumbers: a list containing the atomic numbers of the particles to which the force should be applied. This must have the same length as particleIndices. Element i is the atomic number of the particle specified by element i of particleIndices.

Using a ForceField

The above method requires you to create the System yourself, add particles to it, and build the lists of particle indices and atomic numbers. In simple cases where you want to use XTB as the only force for the entire system, it can be easier to let a ForceField create the System for you.

ff = app.ForceField('xtb/gfn2xtb.xml')
system = ff.createSystem(topology, charge=2, multiplicity=1, periodic=False)

The plugin provides three force field files for the available methods: 'xtb/gfn1xtb.xml', 'xtb/gfn2xtb.xml' and 'xtb/gfnff.xml'.

License

Portions copyright (c) 2023-2024 Stanford University and the Authors.

Authors: Peter Eastman

Contributors:

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.