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mosdef-hub
Flexible storage of chemical topology for molecular simulation
This is a replacement PR for the features requested in #814, which has some commits in the merge history that deviated when switching to ruff linting.
The utilities for converting potentials was not entirely fleshed out. Adding some quick ways to move from OPLS to Fourier potentials, and fixing some of the function naming so it's...
A major feature we want to have robust and wide support for is site (atom) selection. What comes to mind at the moment includes: - [ ] Site name -...
https://docs.python.org/3/library/logging.html Could be useful to specify debugging-level warnings/errors systematically across this package
Port over the old CHARMM/NAMD .prm file writer from mBuild to GMSO. Adding to the savers and allowing for basic charmm style potentials to be written only. TODOS: - [x]...
rigid IDs are `ints` assigned to particles/atoms that signal which rigid body they belong to which is needed when recording rigid body information in HOOMD Frames and/or GSD files. The...
Would be nice to have some more generalized unit systems that certain engines could subclass, as opposed to always calling the different LAMMPS units systems. Mostly a clarity thing.
After switching GMSO to the backend writer in mBuild for HOOMD snapshots and GSD files, I did some poking around about how to hand off the rigid ID when converting...
While working on https://github.com/mosdef-hub/mbuild/pull/1191 in mBuild, I noticed that it should be relatively straight forward to move the [Charmm par writer ](https://github.com/mosdef-hub/mbuild/blob/main/mbuild/formats/par_writer.py)out of `mbuild.formats` and into `gmso.formats`. Moving this to...
mBuild typically infers elements from readers, such as xyz files. As we've updated to GMSO as the backend file handler, that inference is not always handled the same way, with...
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Flexible storage of chemical topology for molecular simulation