/research-scripts

Different run and analysis scripts as described in the research guides.

Primary LanguagePython

research-scripts

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).

LICHEM-tools

This directory contains a number of scripts for working with LICHEM.

QOL-Improvements

This directory contains a number of random scripts that help make life easier.

amber-analysis

This directory contains different scripts relevant to analyzing AMBER MD simulations.

amber-setup

This directory contains a collection of scripts for preparing systems and running simulations with AMBER MD.

general-plotting

This directory contains non-specific plotting scripts.

gromacs-analysis

This directory contains different scripts relevant to analyzing GROMACS MD simulations.

gromacs-setup

This directory contains scripts to help prepare and run GROMACS simulations using AMBER force fields.

other-programs

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.

tinker-analysis

This directory contains different scripts relevant to analyzing TINKER MD simulations.

tinker-params

This directory contains information on building a tinker.key file from an AMBER prmtop file.