Solution-Phase Molecular Dynamics

Goal

Set up and run molecular dynamics (MD) simulations of molecules in explicit solvent. This skill covers three stages: (1) building a solvation box with Packmol, (2) running NPT/NVT MD using MLIPs, and (3) analyzing the trajectory for radial distribution functions (RDFs), coordination numbers, density convergence, and mean-square displacement (MSD).

[!IMPORTANT] This skill bridges gas-phase chem-* skills and condensed-phase mat-* skills by providing workflows for solvation dynamics, liquid structure characterization, and dissolution studies.

1. Prerequisites

• Packmol binary must be installed and on PATH in the base-agent environment.
• RDKit must be available in the base-agent environment (for SMILES → 3D geometry).
• An MLIP backend must be available via MCP tools (MACE, MatGL, or FairChem).

2. MLIP Selection

Refer to the foundation-potentials skill for model selection.