Add forcefield.py with library of FF options; include option to use united atom system #5
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This PR achieves 2 things:
Makes it a little easier to use difference force fields with the addition of
forcefield.py
. This essentially creates classes of different force fields that can be imported and passed intoSystem.apply_forcefield
rather than using foyer directly. The primary motivation for this was to add the opls force field that is slightly modified to work for PPS. I also included GAFF.I added a
united_atom
parameter that can beTrue
orFalse
when initializing theSystem
class. IfTrue
, the hydrogen atoms will be removed, and the mass and charges of the heavy atoms they were bonded to will be be adjust to account for the lost hydrogens. This is all done in theapply_forcefield
method. I think most of our simulations for this project can be UA, which will bump up our TPS performance.To do:
Importing from the forcefield library in
project.py
doesn't seem to be working yet.