Skip to content

Latest commit

 

History

History
100 lines (70 loc) · 4.33 KB

README.md

File metadata and controls

100 lines (70 loc) · 4.33 KB
Raw

GH Actions Status Conda Anaconda Cloud Badge

OpenMM PLUMED Plugin

This project provides a connection between OpenMM and PLUMED. It allows you to bias or analyze an OpenMM simulation based on collective variables.

This plugin requires PLUMED version 2.3b or greater. OpenMM 8.1.0 or greater is required to use v2.0 of this plugin. For previous versions of OpenMM you may use v1.0.

Installing The Plugin

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-plumed

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

Building The Plugin

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.

  5. Set PLUMED_INCLUDE_DIR and PLUMED_LIBRARY_DIR to point to the directories where the PLUMED 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

Simply create a PlumedForce object, passing the PLUMED control script as an argument to the constructor, then add it to your System. For example,

script = """
d: DISTANCE ATOMS=1,10
METAD ARG=d SIGMA=0.2 HEIGHT=0.3 PACE=500"""
system.addForce(PlumedForce(script))

Be aware that PLUMED numbers atoms starting from 1, whereas OpenMM numbers them starting from 0. The example above performs metadynamics based on the distance between atoms 0 and 9 (in OpenMM's numbering system).

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) 2016-2023 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.