Claude Code skills for molecular simulation and computational biochemistry, developed and maintained by the BioKT lab (Theoretical Biochemistry Laboratory) at the University of the Basque Country (UPV/EHU) and the Donostia International Physics Center (DIPC).
The BioKT group works at the intersection of chemical physics and biochemistry, with a focus on protein dynamics, folding, and binding. Research topics include:
- Intrinsically disordered proteins and coupled folding-binding
- Protein conformational transitions studied with optical tweezers and AFM
- Kinetic models of metastable states using master equation approaches (MasterMSM)
- Quantum mechanical investigations of protein–metal interactions
Simulations are run primarily with GROMACS and AMBER, analysed with MDtraj, and enhanced sampling is performed with PLUMED.
| Skill | Description |
|---|---|
gmx-prep |
GROMACS MD simulation preparation: force field setup, solvation, equilibration, production, AWH, H-REMD, umbrella sampling |
gmx-install |
GROMACS source build with PLUMED, GPU (CUDA), and MPI support; includes benchmark testing |
amber-parameterize |
Small-molecule parameterization with AmberTools (antechamber, parmchk2, tleap); GAFF/GAFF2 force fields; GROMACS conversion via acpype |
dft-homo-lumo |
DFT geometry optimisation and HOMO/LUMO frontier orbital analysis using PySCF |
bash-parallelize |
Identify independent work items in a task description or bash loop and run them in parallel using subagents; safety-checks system load before launching |
plumed-us |
Umbrella sampling setup and analysis with PLUMED: multi-window RESTRAINT input files, WHAM analysis, free energy profiles and error bars |
plumed-metad |
Metadynamics setup and analysis with PLUMED: well-tempered metadynamics, free energy surfaces with sum_hills, reweighting, block error analysis, convergence assessment |
plumed-remd |
Replica simulations with PLUMED: umbrella sampling with replica exchange, bias-exchange metadynamics, parallel-tempering metadynamics, trajectory demuxing and WHAM analysis |
Clone this repository and run install.sh to symlink all skills into ~/.claude/skills/:
git clone https://github.com/BioKT/Skills-BIOKT.git
cd Skills-BIOKT
bash install.shTo update on any machine:
git pull && bash install.shInvoke a skill from any Claude Code session:
/gmx-prep
/gmx-install
/gmx-install test
/amber-parameterize
/dft-homo-lumo
/bash-parallelize
/plumed-us
/plumed-metad
/plumed-remd