Individual skill
molecular-dynamics
Runs and analyzes molecular dynamics simulations with OpenMM and MDAnalysis. Sets up protein/small molecule systems, defines force fields, runs energy minimization and production MD, and analyzes trajectories (RMSD, RMSF, contact maps, free energy surfaces). For structural biology, drug binding, and biophysics.
skills/molecular-dynamics/SKILL.md
Source commit 2d2065fb4520fa3f3f2bcf61cff26ec8b7eba4b5
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- Last checked
- Nov 10, 2026
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- 56,757
- Repository last updated
- Nov 9, 2026
- License
- MIT
Observed agent integration: No specific integration evidence. Standard SKILL.md installation does not imply verified compatibility.
- ai-scientist Repository topic
- bioinformatics Repository topic
- chemoinformatics Repository topic
- claude Repository topic
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- claudecode Repository topic
- clinical-research Repository topic
- computational-biology Repository topic
- data-analysis Repository topic
- drug-discovery Repository topic
- engineering Derived category
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# Molecular Dynamics
## Overview
Molecular dynamics (MD) simulation computationally models the time evolution of molecular systems by integrating Newton's equations of motion. This skill covers two complementary tools:
- **OpenMM** (https://openmm.org/): High-performance MD simulation engine with GPU support, Python API, and flexible force field support
- **MDAnalysis** (https://mdanalysis.org/): Python library for reading, writing, and analyzing MD trajectories from all major simulation packages
**Reviewed versions:** OpenMM 8.6.1 and MDAnalysis 2.10.0. Reference-platform
smoke checks use small synthetic systems; GPU performance and scientific convergence
are not established by them. OpenMM latest API pages identify a development build,
so the installed 8.6.1 API is the executable reference.
