========= QM/MM/PME

:Author: John Pederson :Author Email: [email protected] :Project: QM_MM :Date Written: August 27, 2022 :Last Date Modified: August 27, 2022

Summary

This package implements dynamics for the QM/MM/PME method described by John Pederson and Professor Jesse McDaniel:

DOI: 10.1063/5.0087386 <https://aip.scitation.org/doi/10.1063/5.0087386>_

Installation

This software depends on a modified fork of openmm <https://github.com/johnppederson/openmm>_ and a modified fork of psi4 <https://github.com/johnppederson/psi4>_. These modified repositories must be compiled from source.

The modified openmm requires the following dependencies:

• cython
• doxygen
• swig

The modified psi4 requires the following dependencies:

• gcc>=4.9
• gau2grid
• pint
• pydantic
• libxc
• numpy>=1.19.2

The QM/MM repository requires the following additional dependencies:

• lxml
• scipy

Once the modified psi4 and openmm repositories are built, the QM_MM repository may be cloned. No source requires compilation.

Usage

Any python run file should include this directory in its path in order to use this software. An anaconda environment should point towards the modified openmm and psi4 repositories. Required input files include PDB, topology XML, and forcefield XML for the OpenMM interface. All other options may be passed as options in the instantiation of the MMSubsystem, QMSubsystem, and QMMMSystem objects.

Documentation

The documentation for this project can be found here <>_!

Authors

Shahriar Khan

Jesse McDaniel

John Pederson