BIOKT Group
Official@biokt · Donostia-San Sebastián (Spain)
BioKimika Teorikoa Group @ EHU + DIPC
Agent Skills by BIOKT Group
Showing 12 vetted skills indexed across 1 GitHub repositories.
BioKTplumed-us
Run umbrella sampling workflows with PLUMED and GROMACS, including WHAM reweighting and free-energy surface construction.
BioKTtyler
Convert academic PDF folders into a token-efficient Markdown wiki with YAML frontmatter.
BioKTplumed-metad
Automate PLUMED metadynamics setup and analysis for free-energy landscapes.
BioKTbash-parallelize
Parallelize bash tasks across independent items with subagents.
BioKTgmx-prep
Automate GROMACS MD preparation from PDB to production with SLURM templates.
BioKTdft-homo-lumo
Convert SMILES or names into optimized DFT geometries and HOMO/LUMO orbital data.
BioKTamber-parameterize
Automate small-molecule parameterization from SMILES to GAFF2 and GROMACS topologies.
BioKTgmx-install
Automate GROMACS source installation with PLUMED patching and CUDA/MPI configuration.
BioKTbitacora
Log and organize lab-session work in LABNOTEBOOK.md.
BioKTsim-paths
Validate critical simulation file paths on remote machines via SSH before GROMACS/plumed job submission.
BioKTjobs
Track active and completed simulation jobs in a centralized JOBS.md file.
BioKTplumed-remd
Coordinate PLUMED multi-replica simulations for GROMACS umbrella sampling and metadynamics.
Frequently Asked Questions About BIOKT Group
FAQPage SchemaWhat specific research tasks are enabled by BIOKT Group's technical stack?▼
The stack enables molecular dynamics preparation, small-molecule parameterization, and free-energy surface construction. It facilitates the conversion of chemical identifiers into quantum mechanical orbital data and manages multi-replica simulation coordination for complex thermodynamic sampling.
Which personas benefit from integrating these computational research capabilities?▼
Computational chemists, structural biologists, and molecular modelers benefit from these capabilities. The stack is designed for researchers managing high-performance computing environments who require standardized, reproducible paths for GROMACS simulation setup and quantum mechanical geometry optimization.
What are the primary prerequisites for deploying these simulation environments?▼
Deployment requires a Linux-based high-performance computing environment with SLURM workload management. Users must have GROMACS, PLUMED, and relevant quantum chemistry packages installed, alongside SSH access to remote clusters for job submission and file path validation.