Running SMOG simulations 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 OpenMM from Conda.
  2. Submit your PDB file to the SMOG web server and get the GROMACS input files. Currently only the all-atom model is supported in OpenMM. Note that 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 here.
  3. 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