mohebifar / openmm-transformer

A cleaner way to manage custom forces in OpenMM

openmm-transformer

A cleaner way to manage custom forces in OpenMM

This project was initially created to simplify input files for running OpenMM simulations with the Buckingham nonbonded. This package comes with the buckingham force transformer by default.

Transformers

BuckinghamForce

Add a BuckinghamForce tag to your forcefield file using the following format:

<BuckinghamForce bondCutoff="3">
  <Atom type="OW" c6="0.003" c8="0.00003" c10="0.0" a="1600000.0" b="42.00" gamma="35.8967" />
  <Atom type="HW" c6="0" c8="0" c10="0" a="0.0" b="0.0" gamma="0" />
  <Atom type="MW" c6="0" c8="0" c10="0" a="0.0" b="0.0" gamma="0"/>
</BuckinghamForce>

Then in the simulation script use BuckinghamTransformer to prepare the ForceField file for OpenMM's parser:

from openmm_transformer import BuckinghamTransformer
from simtk.openmm import app

with BuckinghamTransformer('my-buckingham-forcefield.xml') as b68:
  forcefield = app.ForceField(b68)