This repository contains examples of the different run and analysis scripts described in the research guides.
See comp-chem-website for explanations.
The majority of these scripts pertain to molecular dynamics (MD), though there are some for quantum mechanics/molecular mechanics (QM/MM).
This directory contains a number of scripts for working with LICHEM.
This directory contains a number of random scripts that help make life easier.
This directory contains different scripts relevant to analyzing AMBER MD simulations.
This directory contains a collection of scripts for preparing systems and running simulations with AMBER MD.
This directory contains non-specific plotting scripts.
This directory contains different scripts relevant to analyzing GROMACS MD simulations.
This directory contains scripts to help prepare and run GROMACS simulations using AMBER force fields.
This directory contains different scripts and configuration files relevant to programs outside of those used for MD or QM/MM. Currently, it contains information for CAVER, gnuplot, and VMD.
This directory contains different scripts relevant to analyzing TINKER MD simulations.
This directory contains information on building a tinker.key file from an
AMBER prmtop file.