Provide GROMACS command reference and workflow guidance for simulations.
npx skills add https://github.com/CharlesHahn/DuIvySkills --skill gromacs
Please help me install this Agent Skill. Skill: gromacs Source: https://github.com/CharlesHahn/DuIvySkills/tree/main/gromacs-skills Command: npx skills add https://github.com/CharlesHahn/DuIvySkills --skill gromacs
This skill provides a comprehensive command reference and workflow guidance for GROMACS simulations, helping users quickly access commands and best practices for setup, execution, and analysis.
Use the gromacs skill to look up a command like gmx rms -h or to follow a complete workflow from pdb2gmx to mdrun.
High-intent search queries and answers about installing and using this skill.
A complete molecular dynamics workflow involves sequence from pdb2gmx for topology generation to mdrun for simulation execution, followed by trajectory processing and energy analysis. This provides step-by-step guidance for protein, membrane, and complex systems.
Trajectory analysis commands such as gmx rms and gmx rmsf process simulation outputs to calculate structural deviations and fluctuations. Post-processing workflows also cover PCA and free energy landscape visualization for protein dynamics.
Yes, a working GROMACS installation is required to execute commands and workflows. You can optionally use local help commands like gmx -h for parameter inspection and access included references for deeper documentation.
Topology setup uses the pdb2gmx command to generate molecular topology files from protein structures. This initial step defines force field parameters and is part of the documented workflow from system setup to production MD.
Energy analysis and visualization for membrane systems use trajectory processing commands to extract and plot energy data. The workflows cover system setup through production MD and post-processing analyses specifically for protein, membrane, and complex systems.
Yes, the workflow guidance includes post-processing analyses for PCA and free energy landscape (FEL) calculations. These analyses follow trajectory processing steps to visualize protein conformational dynamics and energy distributions.
HeshamFSSelect and configure time integration methods for ODE and PDE simulations.
Estrella-231Simulate biomolecular dynamics with OpenMM and analyze trajectories using MDAnalysis.
dralkhPrepare and analyze molecular dynamics simulations with OpenMM and MDAnalysis.
RamanEbrahimiAutomate molecular dynamics simulations and trajectory analysis with OpenMM and MDAnalysis.
