Using SMOG models in OpenMM

Our group has recently added support for running SMOG models in OpenMM.  OpenMM is a modern Molecular Dynamics package that includes full GPU support out of the box and is easy to customize.  In order to use SMOG models in OpenMM, we recommend the following steps:

  1. Get the latest OpenMM code from github (must be at least at least revision fbf193fe366dbd1a9c39eec754f737b42d24acac on April 18th, 2017.  SMOG support is prerelease software, though we expect it to be included for release in the next major version of OpenMM).
  2. Build and install the OpenMM code from step 1 by following instructions on the OpenMM website: 
    http://docs.openmm.org/7.1.0/userguide/library.html#compiling-openmm-fro....  Make sure you include Python support because the SMOG compatibility code is written in Python.  A good test to ensure your code is installed correctly is to run the OpenMM Python self-check:
    1. ​python -m simtk.testInstallation
  3. Submit your PDB file to http://smog-server.org/cgi-bin/GenTopGro.pl and get the GROMACS input files.  Currently only the all-atom model is supported.  Use of the SMOG web server is not required as the SMOG2 standalone software also supports the all-atom model.   Alternatively, you can download the SMOG example model that is found at http://smog-server.org/2ci2.smog.tar.gz
  4. Download our dynamics.py script and call it using the SMOG .gro and .top files as inputs:
    ./dynamics.py your.gro your.top your.dcd