Prepare and analyze molecular dynamics simulations with OpenMM and MDAnalysis.
npx skills add https://github.com/dralkh/seerai --skill molecular-dynamics-dralkh
Please help me install this Agent Skill. Skill: molecular-dynamics Source: https://github.com/dralkh/seerai/tree/main/skills/molecular-dynamics Command: npx skills add https://github.com/dralkh/seerai --skill molecular-dynamics-dralkh
This Skill helps researchers set up, run, and interpret molecular dynamics simulations without manually stitching together multiple tools and analysis steps.
Ask the molecular-dynamics skill to prepare your structure, run equilibration and production, and analyze the trajectory for RMSD, RMSF, and protein-ligand contacts.
High-intent search queries and answers about installing and using this skill.
You can set up and analyze molecular dynamics simulations by building a solvated biomolecular system, assigning force fields, and running energy minimization, equilibration, and production. Trajectory analysis provides RMSD, RMSF, and protein-ligand contact metrics via MDAnalysis.
From an MD trajectory, MDAnalysis calculates structural metrics such as RMSD, RMSF, contacts, secondary structure, principal components, and free energy surfaces to quantify conformational changes and binding-induced flexibility.
OpenMM and PDBFixer support biomolecular system preparation for molecular dynamics by fixing common structure issues, building solvated systems, and assigning force fields for proteins, ligands, membranes, and nucleic acids.
The molecular dynamics workflow supports protein, ligand, membrane, nucleic-acid, and disordered-protein simulations, covering system setup, force-field assignment, periodic boundary conditions, energy minimization, equilibration, and production runs.
To compare binding-induced flexibility, run a production trajectory and analyze it for RMSF and protein-ligand contacts. This trajectory analysis quantifies residue-level structural behavior and flexibility changes upon binding.
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