109 tagged computational chemistry, measured the same way as everything else here.
Browse within: Cheminformatics 57calphad 57openclaw 46
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
Fine-tune a DPA3 model in DeePMD-kit using the PyTorch backend. Use when the user wants to adapt a pre-trained DPA3 model to a new downstream dataset. Supports fine-tuning from a self-trained DPA3 model (.pt checkpoint), from a multi-task pre-trained model, or from a built-in pretrained model downloaded via dp…
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
A command-line tool in AmberTools for preparing small molecules or non-standard residues within GAFF/AMBER-compatible chemical space for molecular mechanics simulations, by automating atom/bond typing, charge generation or import, and force-field–compatible input generation. USE WHEN you are working in AMBER, dealing…
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
A tool and knowledge base for running molecular dynamics (MD) simulations in LAMMPS with the DeePMD-kit plugin. It handles input script preparation, ensemble selection (NVE/NVT/NPT), and job execution via uv or offline binaries. USE WHEN you need to set up, write, explain, or execute a LAMMPS molecular dynamics…
xjtulyc/awesome-rosetta-skills
Skill Claude CodeCodex
Atomic Simulation Environment (ASE) for atomistic simulations: structure building, geometry optimization, NEB, molecular dynamics, and trajectory analysis.
SFETNI/Deep-Matter-Chem-Skills
Skill Claude CodeCodex
This skill covers quantitative post-processing of atomistic molecular dynamics trajectories: loading and preprocessing trajectories from LAMMPS, GROMACS, or ASE; computing structural observables (RDF, coordination numbers, angular distributions, bond orientational order, common-neighbor analysis, centrosymmetry…
SFETNI/Deep-Matter-Chem-Skills
Skill Claude CodeCodex
This skill covers selection, validation, and deployment of interatomic force fields for molecular dynamics: the physical basis and transferability limits of every major functional form (EAM, MEAM, Tersoff, Stillinger-Weber, Buckingham, COMB, ReaxFF, AMBER, CHARMM, OPLS, GROMOS, and ML potentials); parameter-file…
SFETNI/Deep-Matter-Chem-Skills
Skill Claude CodeCodex
This skill covers reactive molecular dynamics (reactive MD) using LAMMPS with the ReaxFF and COMB force fields: force-field selection and parameter provenance, charge equilibration (QEq) setup and diagnostics, timestep and thermostat selection for reactive systems, thermal protocols for reaction sampling, reaction…
Skill Claude CodeCodex
Use when working on classical biomolecular molecular dynamics with GROMACS: system setup, pdb2gmx/topology preparation, ligand parameterization, solvation and ions, energy minimization, NVT/NPT equilibration, production MD, trajectory analysis, MM/PBSA-style post-processing, .mdp parameter review, GROMACS command…
Skill Claude CodeCodex
Use when creating, improving, or troubleshooting publication-ready molecular structure figures with PyMOL: protein cartoons, ligand binding pockets, surfaces, electrostatic-style views, hydrogen bonds, labels, structure alignments, MD representative snapshots, transparent PNG export, ray tracing, journal-quality…
Skill Claude CodeCodex
Use when creating reusable PyMOL figures for protein-protein or chain-chain interfaces from PDB/MD snapshot files, especially when the user wants only protein kept, water/ions/ligands removed, inter-chain hydrogen-bonding residues shown as sticks, green dashed hydrogen bonds, chain-colored cartoons and labels…