QM/MM/PME

Author:	John Pederson
Author Email:	jpederson6@gatech.edu
Project:	QM_MM
Date Written:	March 28, 2022
Last Date Modified:	May 26, 2022

Summary

This package implements single-point energy calculations for the QM/MM/PME method described by John Pederson and Professor Jesse McDaniel:

DOI: 10.1063/5.0087386

Installation

This software depends on a modified fork of openmm and a modified fork of 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

Jesse McDaniel

John Pederson