molecular-simulations 0.3.18

A small package for building molecular systems using the AMBER \ force field and deploying OpenMM simulations on HPC clusters using Parsl.

molecular-dynamics repository README

molecular-dynamics 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 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/