LICHEM with Tinker and Gaussian: Setup

LICHEM requires an underlying installation of the programs you intend to do calculations with.

QM Wrappers

• Gaussian (Gaussian, g09, g16)
• PSI4 (PSI4)
• NWChem (NWChem)

MM Wrappers

• Tinker (TINKER keyword will work for any 7 or 8 series; Tinker HP requires poledit from another version)
• LAMMPS (LAMMPS)

In the case of this tutorial, you will need access to Gaussian (either 09 or 16) and Tinker7.1.

Installing TINKER

The Tinker executables and source code are available on their site.

Install Tinker 7.1.3.

WARNING

Tinker parameter files are different between 7.1 and various versions of Tinker 8! You MUST modify the parameter files associated with the version you are going to use for QM/MM!

Tip

If you have multiple versions of Tinker installed, export a global variable to the bin of each edition name.

Add this to your ~/.bashrc

export Tinker7=/home/$USER/bin/tinker7/bin

and then call the program with $Tinker7/xyzedit.

Gaussian

If you are using Gaussian on an HPC cluster, simply load the module for the version you would like to use. You may need to be added to the user’s group first.

For TACC resources, this means you will need to fill out a usage agreement.

Installing LICHEM

The instructions for installing LICHEM are included here for convenience.

$ mkdir LICHEM
$ git clone https://github.com/CisnerosResearch/LICHEM.git ./LICHEM/
$ ./configure
$ make install

Python 3

This tutorial also uses Python 3 code to make setting up LICHEM simulations easier. We recommend an Anaconda installation of Python 3.

• Video of Windows Install
• Video of MacOS Install
• Using conda to install packages

The scripts we will use require the parmed, numpy, pandas, and MDAnalysis packages to be installed. The Anaconda installation should include numpy and pandas.

$ conda install -c omnia parmed
$ conda install numpy
$ conda install pandas
$ conda config --add channels conda-forge
$ conda install mdanalysis