Analyze and visualize GROMACS MD outputs including XVG, XPM, and NDX files.
npx skills add https://github.com/CharlesHahn/DuIvySkills --skill duivytools-skills
Please help me install this Agent Skill. Skill: duivytools-skills Source: https://github.com/CharlesHahn/DuIvySkills/tree/main/duivytools-skills Command: npx skills add https://github.com/CharlesHahn/DuIvySkills --skill duivytools-skills
DuIvyTools provides a unified toolkit to analyze and visualize GROMACS MD outputs (XVG, XPM, NDX), enabling researchers to interpret simulation results quickly and reliably.
Install DuIvyTools with pip: pip install DuIvyTools Then run example commands such as:
High-intent search queries and answers about installing and using this skill.
You can visualize GROMACS RMSD and RMSF data by running the xvg_show command on your XVG files. This automates the plotting process to accelerate interpretation of your molecular dynamics simulation results.
Yes, you can plot DCCM and FEL matrices from GROMACS XPM outputs. The xpm_show command visualizes XPM matrix data, enabling quick and reliable interpretation of dynamic cross-correlation and free energy landscapes.
Analyzing hydrogen bonds and energy trends from MD simulations is best handled by automating XVG data visualization. This provides a unified toolkit to interpret energy fluctuations and hydrogen bond stability quickly across simulation runs.
Yes, this GROMACS analysis toolkit supports batch processing for multiple simulation runs. It applies consistent styling across all results, ensuring reliable comparison of outputs like RMSD, gyrate, and secondary structure data.
You generate Ramachandran plots and secondary structure visualizations by processing your GROMACS outputs with dedicated commands. It handles DSSP XPM matrix visualization to analyze protein backbone dihedral angles and structural changes.
Yes, you need Python installed because this is a Python-based toolkit. You install it via pip and run documented commands to automate the analysis and visualization of your GROMACS MD outputs.
CharlesHahnAnalyze GROMACS protein trajectories for RMSD, RMSF, DCCM, and FEL plots.
jaechang-hitsAnalyze molecular dynamics trajectories with MDAnalysis for RMSD, RMSF, and PCA.
CharlesHahnProvide GROMACS command reference and workflow guidance for simulations.
DrugClawGenerate static and interactive scientific plots from research data using Python libraries.
