Team Mayes & Blue

che_696

Website for the ChemE data science course

atesa

Python program for automating the "Aimless Transition Ensemble Sampling and Analysis" (ATESA) aimless shooting workflow on PBS/TORQUE or Slurm.

best_practice_pmf

Best Practices document to be submitted to the Living Journal of Computational Molecular Science

atesa_OLD

Old version of ATESA, a Python program for automating Aimless Transition Ensemble Sampling and Analysis (ATESA) with the Amber molecular simulations package

gaussian_wrangler

Package of scripts to improve efficiency, accuracy, reproducibility, and reliability when using Gaussian to compute QM calculations

hartree

Tools for Processing Computational Chemistry Data

jobtpl

A set of templating tools for generating and submitting Torque jobs

md_utils

A variety of scripts to aid MD simulations, especially with Lammps.

GoodVibes

Calculate quasi-harmonic free energies from Gaussian output files with temperature and other corrections

umich_che344

Handy Python scripts for ChE344

aimless

Python script for running aimless shooting with Amber

arthritis_proj_demo

Demo of making a project from a cookiecutter template for che_696

auto_cgui

Automatic CHARMM-GUI browser interaction with Python

basic_simulation_training

A document for the Living Journal of Computational Molecular Science (LiveCoMS) which describes basic training for molecular simulations (oriented towards molecular dynamics (MD)), providing some training itself and linking out to other helpful information elsewhere. The intent is that this provide information on the prerequisites which will be required for understanding/following many of the other "best practices" documents being prepared.

che696_examples

Some example to help students make their own projects

common-python

Common Python functions and constants used in Team Mayes & Blue projects.

common_wrangler

a home for utilities that are general file manipulation scripts (e.g. renaming files) and common methods for multiple scripts in gaussian_wrangler and md_wrangler

cookiecutter-compchem

Python-centric Cookiecutter for Molecular Computational Chemistry Packages

isEE

Incomplete work on automated "in silico Enzyme Evolution"

lignin-kmc

pucker_prog_data

Data for the python program used for the Pucker Project

qm_utils

Tools for QM projects in Team Mayes & Blue

team-site