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molecular-dynamics

k-dense-ai/scie…t-skills

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.

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安装命令

npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill molecular-dynamics

SKILL.md

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.

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