Automate GROMACS MD preparation from PDB to production with SLURM templates.
npx skills add https://github.com/BioKT/Skills-BIOKT --skill gmx-prep
Please help me install this Agent Skill. Skill: gmx-prep Source: https://github.com/BioKT/Skills-BIOKT/tree/main/gmx-prep Command: npx skills add https://github.com/BioKT/Skills-BIOKT --skill gmx-prep
GROMACS MD preparation is a complex, error-prone process that requires careful sequencing of topology building, solvation, ion placement, and initial equilibration. This Skill provides an end-to-end blueprint to standardize and reproduce MD workflows from pdb to production runs.
Install and tailor the base workflow to your system, then run the provided scripts in order to generate ready-to-run MD configurations.
High-intent search queries and answers about installing and using this skill.
Automating GROMACS MD preparation involves running a sequenced workflow of pdb2gmx, editconf, solvate, genion, energy minimization, NVT, NPT, and production setup. This Skill standardizes that pipeline to generate ready-to-run MD configurations.
Standardizing GROMACS topology building and solvation across multiple systems requires applying consistent mdp parameters and a structured workflow. This Skill provides an end-to-end blueprint ensuring comparable results across simulations and projects.
Yes, the GROMACS preparation workflow applies to researchers running molecular simulations across IDPs, folded proteins, and complex assemblies. It standardizes equilibration and ion placement for diverse molecular systems.
Yes, SLURM job script templates are included for submitting GROMACS production runs to HPC clusters. These templates accompany the standard preparation pipeline to streamline job execution.
Errors during GROMACS energy minimization or NPT equilibration often stem from incorrect ion placement or unstandardized mdp parameters. This Skill standardizes the solvation, genion, and equilibration sequence to prevent such setup errors.
CharlesHahnAnalyze GROMACS protein trajectories for RMSD, RMSF, DCCM, and FEL plots.
SciMate-AIAutomates end-to-end HPC GROMACS workflows from preprocessing to analysis.
CharlesHahnProvide GROMACS command reference and workflow guidance for simulations.
matsunagalabAutomate molecular dynamics preparation workflows from structure acquisition to topology generation.
