drug-protein-ligand-md
OfficialRun OpenMM protein–ligand NPT MD end-to-end
Education & Research#drug discovery#protein-ligand#molecular dynamics#openmm#NPT simulation#trajectory generation#checkpoint restart
Authorlearningmatter-mit
Version1.0.0
Installs0
System Documentation
What problem does it solve?
This Skill automates running a complete protein–ligand molecular dynamics (MD) simulation using OpenMM, so you can generate trajectories and checkpoints for downstream analysis without manually chaining minimization, equilibration, and production steps.
Core Features & Use Cases
- End-to-end MD pipeline: performs energy minimization, restrained NVT equilibration, restrained-then-released NPT equilibration, and NPT production.
- OpenMM-ready inputs & outputs: consumes
system.xmlandcomplex_solvated.pdb, and producesproduction.dcd,final_state.xml, and logs/provenance for restart and analysis. - Replicates support: run multiple independent replicates with different seeds to assess statistical confidence (e.g., pose stability, binding-pocket retention).
Quick Start
Run an NPT production MD from the system bundle generated by drug-complex-system-builder for temperature 300 K and output results to md/run/.
Dependency Matrix
Required Modules
openmm
Components
scripts
💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: drug-protein-ligand-md Download link: https://github.com/learningmatter-mit/AtomisticSkills/archive/main.zip#drug-protein-ligand-md Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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