Metadata-Version: 2.4
Name: molecular_simulations
Version: 0.3.20
Summary: A small package for building molecular systems using the AMBER \ force field and deploying OpenMM simulations on HPC clusters using Parsl.
Project-URL: Homepage, https://github.com/msinclair-py/molecular-dynamics
Project-URL: Issues, https://github.com/msinclair-py/molecular-dynamics/issues
Author-email: Matt Sinclair <msinclair@anl.gov>
License-Expression: MIT
License-File: LICENSE
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.10
Requires-Dist: black-pdbfixer
Requires-Dist: mdanalysis>=2.7
Requires-Dist: mdtraj
Requires-Dist: natsort
Requires-Dist: numba
Requires-Dist: openmm>=8.0
Requires-Dist: parmed
Requires-Dist: parsl>=2024.1.29
Requires-Dist: polars
Requires-Dist: pydantic
Requires-Dist: pyyaml
Requires-Dist: scikit-learn
Requires-Dist: seaborn
Provides-Extra: dev
Requires-Dist: numpy>=1.22; extra == 'dev'
Requires-Dist: pytest-cov; extra == 'dev'
Requires-Dist: pytest>=7.0; extra == 'dev'
Provides-Extra: docutils
Requires-Dist: docutils; extra == 'docutils'
Requires-Dist: sphinx; extra == 'docutils'
Requires-Dist: sphinx-rtd-theme; extra == 'docutils'
Provides-Extra: ligand
Requires-Dist: openbabel; extra == 'ligand'
Requires-Dist: rdkit; extra == 'ligand'
Description-Content-Type: text/markdown

# molecular-dynamics repository README
[molecular-dynamics](https://molecular-simulations.readthedocs.io/en/latest/index.html) 
is a collection of python utilities for MD simulation building, 
running and analysis.

Capable of building molecular dynamics systems using the AMBER forcefield
ecosystem. Available forcefields include: fixed-charge forcefields (ff19SB 
for proteins, OL21 for DNA, and OL3 for RNA), ff15ipq polarizable forcefield,
and the ability to parameterize small molecules using GAFF2. In all explicit
systems OPC water is used with the exception of polarizable systems where a
polarizable water model is used (SPC/Eb). 
Loosely tested support for implicit solvent systems as well.

Also bundled in this library are tools for analyzing molecular simulations
including: correlation analysis, interaction energy, residue energy footprinting, 
automatic clustering, an MDAnalysis-based SASA and RSASA methods and more.

## Installation
Easily installed via pip. PyPI page: https://pypi.org/project/molecular-simulations/

`pip install molecular-simulations`

## Package details
Simulations are performed using OpenMM version >= 8 due to CUDA versioning
on ALCF Polaris. Note that due to some scaling issues reported by users,
OpenMM versions 8.0-8.1 suffer from slow integration times for larger
systems. All MD simulations are deployed on a PBS scheduler via 
[Parsl](https://parsl.readthedocs.io/en/stable/) but
with some minor tweaking of the Parsl configuration object they can be
deployed on theoretically any HPC cluster/job scheduler. Jobs can also
be run locally without the need for Parsl (example coming soon).

## Usage
See `examples` for how to run a few of the tools contained within.

See Parsl documentation for further examples of how to run on other HPC resources. https://parsl.readthedocs.io/en/stable/
