chem-solution-md
OfficialRun explicit-solvent MD and extract structure.
Education & Research#trajectory analysis#ase#packmol#molecular dynamics#mlip#explicit solvent#radial distribution function
Authorlearningmatter-mit
Version1.0.0
Installs0
System Documentation
What problem does it solve?
This Skill helps you set up and analyze explicit-solvent molecular dynamics for solutes in liquid environments, so you can quantify solution structure and dynamics rather than relying on qualitative inspection.
Core Features & Use Cases
- Build explicit-solvent boxes using Packmol with solute geometry generated from SMILES (via RDKit) or loaded from structure files.
- Run MLIP-based MD in NPT (density equilibration) followed by NVT (production) through MCP MD tools.
- Analyze trajectories by computing RDFs, coordination numbers, density convergence, and (optionally) MSD from ASE trajectories.
Quick Start
Use the chem-solution-md skill to build a solvated box, run NPT→NVT MD with an available MLIP MCP backend, and produce RDF/density/MSD outputs for your specified solute and solvent.
Dependency Matrix
Required Modules
asenumpymatplotlibpymatgenrdkitpyyaml
Components
scriptsassetsreferences
💻 Claude Code Installation
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Please help me install this Skill: Name: chem-solution-md Download link: https://github.com/learningmatter-mit/AtomisticSkills/archive/main.zip#chem-solution-md Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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