Installation of Foyer and required tools
conda install -c omnia -c mosdef parmed foyer pytest
Creating a new force field:
- 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/
- Create your force field
.xmlfile based on the OpenMM
.xmlformat and add foyer style SMARTS strings to define your atom types. Example force field files:
- 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=lineis recommended, as this will perform checking of your
.xmlfile for proper syntax and ensure that all atom types references are defined.
- Generate your own DOI via Zenodo
- 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)]
< Add specific notes about parameters, e.g., if a set of parameters comes verbatim from prior work, provide details and a DOI >
< 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.