Skill Claude CodeCodex
A usage guide for DuIvyProcedures, a batch-analysis tool for molecular-dynamics trajectories. It uses YAML configuration files to run many analyses and produce charts and data from multiple trajectories.
Skill Claude CodeCodex
A command-line guide for DuIvyTools, a toolkit for analysing and plotting molecular-dynamics simulation data. It covers protein-motion measurements, interaction data, matrix plots, statistics, and file conversion.
Skill Claude CodeCodex
A method for using GROMACS molecular-dynamics trajectories to estimate how strongly two molecules bind. GROMACS is software that simulates molecular motion, and gmxMMPBSA is a tool for estimating binding free energy from those simulations.
Skill Claude CodeCodex
A workflow guide for analysing protein molecular-dynamics simulations, which model how atoms move over time. It describes procedures for correcting periodic-boundary artefacts, measuring motion and flexibility, and studying structural changes and interactions.
Skill Claude CodeCodex
A command reference for GROMACS, software that runs and analyses molecular-dynamics simulations. It covers preparing molecular systems, running simulations, processing trajectories, and measuring structural and interaction properties.
Skill Claude CodeCodex
A workflow guide for creating GROMACS force-field definitions for non-standard amino-acid residues, such as a chemically modified cysteine. A force field is the set of rules and parameters used to calculate molecular interactions in a simulation.