lammps

Atomistic structure manipulation, file-format conversion, supercells, surfaces, and geometry optimization with ASE

1 skill

Bayesian optimization for expensive material and molecular properties using Ax and BoTorch

1 skill

Generate, validate, and debug CP2K input files for periodic DFT, AIMD, and geometry optimization

1 skill

Analyze MD trajectories: RDF, MSD, order parameters, structure factor, PMFT, Voronoi, and clustering

1 skill

Biomolecular MD setup, execution, and analysis with GROMACS

1 skill

Read and write LAMMPS data and dump files, with LAMMPS/GSD interconversion

1 skill

Real-time rope/cable physics using Position-Based Dynamics (PBD), Verlet integration, and constraint solvers. Expert in quaternion math, Gauss-Seidel/Jacobi solvers, and tangling detection. Activate on 'rope simulation', 'PBD', 'Position-Based Dynamics', 'Verlet', 'constraint solver', 'quaternion', 'cable dynamics', 'cloth simulation', 'leash physics'. NOT for fluid dynamics (SPH/MPM), fracture simulation (FEM), offline cinematic physics, molecular dynamics, or general game physics engines (use Unity/Unreal built-ins).

1 skill

MDClaw skills and CLI tools for preparing systems, running MD, analyzing trajectories, and packaging atomistic evidence

14 skills · hooks

Medicine Design Software Development: the drug discovery pipeline and where computation actually helps, targets and modalities, what makes a molecule a drug, molecular representation, cheminformatics toolkits, data sources and their quality problems, splitting and leakage, protein structure and structure prediction, docking, molecular dynamics, free energy methods, QSAR and property prediction, ADMET prediction, generative models, active learning and the DMTA loop, benchmarks, validation that means something, pipeline engineering, compute, reproducibility, GxP and computer system validation, and software as a medical device.

6 skills

Agentic systematic coarse-graining

14 skills · 2 commands · 2 agents · hooks