chem-solution-md

Set up explicit-solvent molecular dynamics by building a Packmol solvation box, running MLIP-driven NPT equilibration followed by NVT production, and post-processing the ASE trajectory to extract radial distribution functions and coordination numbers.

MLIP-driven solution-phase MD first runs an NPT ensemble step to equilibrate solvent density, then switches to an NVT ensemble for production sampling, after which trajectory post-processing yields density convergence data and structural observables.

Yes, Packmol constructs explicit-solvent boxes by packing solvent molecules around a solute geometry generated from a SMILES string via RDKit or loaded directly from an existing structure file.

Yes, trajectory post-processing computes density convergence, radial distribution functions, coordination numbers, and optionally mean square displacement to characterize both structural and dynamic properties of the solution phase.

Yes, the workflow requires an MLIP MD backend exposed via MCP tools to drive NPT and NVT simulations and generate ASE trajectories for subsequent structural and dynamic analysis.