Tools to prepare an OpenMM simulation
This is intended to be a simple package for getting OpenMM simulations up and running; i.e., this includes some scripts to help get from a bare file (like a .pdb or a .gro) to running MD. My general approach is to use a Jupyter notebook to do the setup interactively. I try to ensure that all steps are achieved programmatically, in order to facilitate reproducibility.
The beauty of OpenMM is that, as a library, it is customizable to your
individual needs. Therefore, many people end up writing little wrappers that
facilitate their own workflows. These are my wrappes. They are intended to
simplify some common tasks, but will not work with all setups. In many cases
you may need to write custom setup code, but that can often be based on code
in prepomm.
This package may rely on (and certainly does not replace) several other useful packages for working with OpenMM, including:
Mostly, this chains things together from those packages (and from OpenMM), and it provides a few conveniences that aren't built into any of those tools.
FFModel: convenience class for working with force fieldsmax_atom_distance: fast MDTraj-based code for identifying maximum distance between atoms (useful to setting box size)- functions for creating rhombic dodecahedral box vectors
- automatic protocols for adding hydrogens/solvating, as well as running various equilibration simulations
- PLANNED: sanity checks on your PDB (correct termination, reasonable box size, etc.) These will give better error messages than the default OpenMM errors.
Note that if these features are included into other packages, the implementation here may be removed. This repository isn't intended to be a permanent project; just a central location to maintain a set of useful tools that I couldn't find elsewhere.
The recommended installation is to do a developer install. Clone it (or your
fork of it, if you think you might contribute changes), change into the
directory with setup.py, and run:
pip install -e .Depending on your Python installation, you may need to preface that command
with sudo.