GROMACS Protein MD Setup

Set up and run a GROMACS MD simulation of a protein from a PDB entry or an uploaded structure.

by Temple Compute

W-03 · GROMACS Protein MD Setup

Set up and run a GROMACS MD simulation of a protein from a PDB entry or an uploaded structure.

Domain: BioExcel Building Blocks

Overview

Runs GROMACS with the CHARMM36 force field on a protein (default hen egg-white lysozyme, PDB 1AKI): topology, solvation, NaCl ions, minimization, NVT and NPT equilibration, free production MD, and trajectory re-centering. The workflow has 17 tasks.

Pipeline

fetch_pdb          Download pdb_id or use the uploaded structure
fix_side_chain     Model missing side-chain atoms
build_topology     pdb2gmx, CHARMM36
editconf           Cubic box
solvate            SPC water
grompp_ions ──► genion               Neutralizing NaCl
grompp_minimize ──► mdrun_minimize   Steepest-descent minimization
grompp_nvt ──► mdrun_nvt             NVT equilibration, restrained
grompp_npt ──► mdrun_npt             NPT equilibration, restrained
grompp_free ──► mdrun_free           Free production MD
gmx_image          Re-center, fix periodic boundary artifacts
gmx_trjconv_str    Extract final dry structure

Inputs / Outputs

Input: pdb_id (RCSB code) or, when empty, the structure upload.
Outputs: results/downloaded.pdb, fixed.pdb, system.gro, pdb2gmx_top.zip, boxed.gro, solvated.gro, ionized.gro, minimized.gro, nvt.gro, npt.gro, md.gro, md.trr, imaged.trr, dry.gro.

Parameters

| id | Default | Meaning | |---|---|---| | pdb_id | 1AKI | RCSB PDB code; clear it to use structure | | structure | examples/1aki.pdb | Structure used when pdb_id is empty | | box_padding_nm | 1.0 | Minimum protein-to-box-edge distance (nm) | | ion_concentration_m | 0 | NaCl added on top of neutralizing ions (M) | | equilibration_steps | 5000 | Steps per restrained equilibration stage (2 fs/step) | | production_steps | 50000 | Steps of the free production run (2 fs/step) |

Force field, thermostat and restraints are set in configs/*.yaml.