duivytools_skill

Overview

This skill provides a command-line toolkit for visualizing and processing GROMACS xvg and xpm files and managing related MD analysis tasks. It includes 30+ focused commands for plotting, converting, comparing, and exporting simulation result files, plus utilities for index handling and mdp template generation. The tool emphasizes fast, scriptable workflows for routine molecular dynamics post-processing.

How this skill works

Commands read standard GROMACS output formats (xvg, xpm, ndx, dat, gro) and produce plots, converted data files, or modified index/mdp files. You can choose columns, ranges, interpolation, and plotting engine (matplotlib, plotly, gnuplot, plotext). Many commands support batch input, group-wise operations, sliding averages, and CSV export for downstream analysis.

When to use it

• Visualize time series (XVG) data like RMSD, radius of gyration, energy traces.
• Inspect and convert free-energy or contact maps stored as XPM into CSV/DAT for further analysis.
• Compare multiple simulation runs, compute averages and plot error bars or violin plots across replicates.
• Manipulate index files (NDX): add, split, list, or remove duplicate groups before production analysis.
• Generate basic mdp templates as starting points for GROMACS runs or compute interaction energies between components.

Best practices

• Preview with small data ranges (-b/-e) before plotting long trajectories to validate parameters.
• Specify columns (-c) and labels (-l, -x, -y, -z) explicitly to avoid ambiguous plots when combining files.
• Choose plotting engine by target use: matplotlib for publication-ready figures, plotly for interactive inspection, plotext for quick terminal checks.
• Use -ns/--noshow when running in batch or CI to save files without opening viewers.
• After generating an mdp template, always edit parameters manually to match your system and simulation goals.

Example use cases

• Quickly plot RMSD and gyration from two runs: dit xvg_show -f rmsd.xvg gyrate.xvg.
• Convert a 2D free-energy XPM to CSV and convex-slice it for external plotting: dit xpm2csv -f FEL.xpm -o FEL.csv.
• Compare energy components across replicates with sliding averages and CI: dit xvg_compare -f energy.xvg -c 1,3 -smv CI -ws 100.
• Create DSSP-style XPM and sc.xvg from modern dssp output for legacy pipelines: dit dssp -f dssp.dat -o dssp.xpm.
• Produce a publication figure: interpolate XPM, set colormap and contour mode, and export to high-res image using matplotlib engine.