robinellison/openmm-setup

An application for configuring and running simulations with OpenMM

OpenMM Setup

This is an application for configuring and running simulations with OpenMM. It provides a graphical interface for selecting input files, cleaning up PDB structures, and setting simulation options. It can then either save a script for running the simulation later, or directly run the simulation itself.

Dependencies

OpenMM Setup is a Python application. It requires the following software to be installed:

• OpenMM
• PDBFixer
• Flask

If you are using Anaconda Python or Miniconda, you can install all of these with a single command:

conda install -c omnia openmm pdbfixer flask

Using OpenMM Setup

To install OpenMM Setup, clone this repository, then type

python setup.py install

You can then execute it by typing

openmm-setup

The user interface is displayed through a web browser, but it is still a single user desktop application, not a web application. It should automatically open a web browser displaying the user interface. If for any reason that does not happen, open a browser yourself and point it to the address displayed in the console window (usually http://127.0.0.1:5000).