Getting Started

Installation of Foyer and required tools

conda install -c omnia -c mosdef parmed foyer pytest

Creating a new force field:

1. Duplicate the force field template. This can be done in various ways:

   • Use the "Import repository" function on github.com (in the "+" at top right) to import the template https://github.com/mosdef-hub/forcefield_template
   • Or, follow the documentation on this page: https://help.github.com/articles/duplicating-a-repository/

2. Create your force field .xml file based on the OpenMM .xml format and add foyer style SMARTS strings to define your atom types. Example force field files:

   • https://github.com/chrisiacovella/OPLSaa_perfluoroalkanes

3. Optionally, add example molecules with correct atomtypes defined as test cases. Execute the testing script using py.test -v --tb=line

   • Note, even if test molecules are not created, running py.test -v --tb=line is recommended, as this will perform checking of your .xml file for proper syntax and ensure that all atom types references are defined.

4. Generate your own DOI via Zenodo

   • https://guides.github.com/activities/citable-code/

5. Update the link to the Zenodo DOI badge

   • 

The text above can be removed upon publishing a forcefield, but please be sure to include the following information in the README:

[Title of your forcefield]

• Source: [Journal reference(s) if parameters are published (include DOI link)]

• Forcefield file initially created [DATE] by [Creator(s)]

Source Notes:

< Add specific notes about parameters, e.g., if a set of parameters comes verbatim from prior work, provide details and a DOI >

Additional Notes:

< Add any other relevant information. Also for consistency, please define conversion factors used. Note that we strongly suggest the following unit conversions defined in OpenMM, e.g.: >

• PI is defined as 3.141592653589 for conversion to radians.
• kcal/mol to kJ/mol conversion factor is defined as 4.184.

Force field DOI