# 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/
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"description": "# molecular-dynamics repository README\n[molecular-dynamics](https://molecular-simulations.readthedocs.io/en/latest/index.html) \nis a collection of python utilities for MD simulation building, \nrunning and analysis.\n\nCapable of building molecular dynamics systems using the AMBER forcefield\necosystem. Available forcefields include: fixed-charge forcefields (ff19SB \nfor proteins, OL21 for DNA, and OL3 for RNA), ff15ipq polarizable forcefield,\nand the ability to parameterize small molecules using GAFF2. In all explicit\nsystems OPC water is used with the exception of polarizable systems where a\npolarizable water model is used (SPC/Eb). \nLoosely tested support for implicit solvent systems as well.\n\nAlso bundled in this library are tools for analyzing molecular simulations\nincluding: correlation analysis, interaction energy, residue energy footprinting, \nautomatic clustering, an MDAnalysis-based SASA and RSASA methods and more.\n\n## Installation\nEasily installed via pip. PyPI page: https://pypi.org/project/molecular-simulations/\n\n`pip install molecular-simulations`\n\n## Package details\nSimulations are performed using OpenMM version >= 8 due to CUDA versioning\non ALCF Polaris. Note that due to some scaling issues reported by users,\nOpenMM versions 8.0-8.1 suffer from slow integration times for larger\nsystems. All MD simulations are deployed on a PBS scheduler via \n[Parsl](https://parsl.readthedocs.io/en/stable/) but\nwith some minor tweaking of the Parsl configuration object they can be\ndeployed on theoretically any HPC cluster/job scheduler. Jobs can also\nbe run locally without the need for Parsl (example coming soon).\n\n## Usage\nSee `examples` for how to run a few of the tools contained within.\n\nSee Parsl documentation for further examples of how to run on other HPC resources. https://parsl.readthedocs.io/en/stable/\n",
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