This repository contains scripts, programs, and data files used with the "Computational Chemistry" playlist on the TMP Chem YouTube channel. Primary language is Python3, with toy programs to demonstrate modeling and analysis methods. Repository is always subject to change, and no guarantees are made of the correctness of output.
- Getting started
- Prerequisites
- Installation
- Running the tests
- Running the scripts
- Author
- Acknowledgments
Most recent version of project is located in TMP Chem GitHub account. Download by following instructions for Git clone from GitHub. Requires a terminal, IDE, etc. to execute Python scripts and ability to write to file system within project directories.
Requires Python 3.5 or greater for script execution. Requires access to numpy and matplotlib modules. All prerequisites can be met by downloading and using Python from most recent Anaconda distribution.
No additional installation necessary after cloning the repository.
To run tests for a project, go to the script directory for that project,
[top_level_path]/scripts/[project]. If present, execute run_tests.py
for the project.
python run_tests.py
Depending on print level setting in run_tests, each subtest may print
success or failure message (with or without values and reference). If
all tests pass for a function, function receives a test pass. If all
functions pass, the overall unit test receives a pass, and the scripts
are ready to execute. If failed, search recursively for failure source.
Tests are a work in progress, and may not be present or complete.
Open an issue to give feedback or report bugs.
As of 16 Feb 2017, repository contains two projects: geometry_analysis,
and molecular_mechanics.
The geometry_analysis project contains scripts which take an xyz-format
molecular geometry file as input, and output to screen associated
geometry data, including bond lengths, bond angles, torsion angles,
out-of-plane angles, center of mass, and/or moment of inertia, etc. Sample
xyz files are located in [top_level_path]/geom/xyz directory.
The molecular_mechanics project contains scripts to compute molecular
mechanics energy of a system (mm.py), molecular dynamics trajectories
(md.py), Metropolis Monte Carlo ensembles (mc.py), and optimize
molecular coordinates to potential energy minima (opt.py).
The energy function and parameters in all cases is based on AMBER FF94.
Cornell et. al,
J. Am. Chem. Soc. 1995, 117, 5179-5197.
doi.org/10.1021/ja00124a002
Energy function in Equation 1. Atom types in Table 1. Parameter values
in Table 14. Download AmberTools15 from here. After unzipping,
parameters located in amber14/dat/leap/parm/parm94.dat.
Sample input files for mm are located in
[top_level_path]/geom/[file_type] directories, where file_type] is
xyzq or prm. Sample input files for md and mc are located in
[top_level_path]/geom/sim directory. Output files for each are
demonstrated in samples, and may be written to any accessible file
name.
The sole author of this package is Trent M. Parker.
- Email:
tmpchemistry@gmail.com - LinkedIn: https://www.linkedin.com/in/tmpchem
- Youtube: https://www.youtube.com/tmpchem
The author wishes to thank the following individuals: Dr. Michael S. Marshall, for encouraging him to learn the Python language; Dr. Lori S. Burns, for encouraging him to conform to style guidelines for readable Python code; Dr. Michael A. Lewis, for providing the inspiration for the author to initiate studies in this field; and Dr. C. David Sherrill, for providing an enormous number of opportunities to continue to learn and grow as a scientist and a person.