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Tutorials

Follow along with full end-to-end builds, including AlphaFold 3 predictions and GROMACS production runs.

AlphaFold3 → GROMACS heterodimer MD workflow (CXCL4/CXCL12)

This tutorial walks through a complete end-to-end workflow for taking two protein sequences, predicting their heterodimer structure with AlphaFold 3, and running a full molecular dynamics simulation in GROMACS.

The video covers sequence preparation, AF3 prediction, building the system in GROMACS, solvation, ion addition, energy minimization, NVT/NPT equilibration, and production MD.

Context: simulating the CXCL4/CXCL12 heterodimer with AlphaFold 3 structure predictions and a full solvated, neutralized GROMACS setup.

Highlights

  • Sequence prep, AlphaFold 3 heterodimer prediction, and system building
  • Boxing, solvation, ionization, and restrained minimization
  • NVT/NPT equilibration through to 100 ns production

Produced by Bhargava Systems Research Inc. to make advanced computational biology methods accessible, transparent, and usable for students and researchers.

Build and solvate the heterodimer

gmx pdb2gmx -f input.pdb -o complex.gro -p topol.top -i posre.itp ignh -ter

gmx editconf -f complex.gro -o boxed.gro -c -d 1.0 -bt dodecahedron

gmx solvate -cp boxed.gro -o solv.gro -p topol.top

Ionization setup

ions_em.mdp
integrator      = steep
emtol           = 1000
nsteps          = 500
cutoff-scheme   = Verlet
coulombtype     = PME
rcoulomb        = 1.2
vdwtype         = cut-off
rvdw            = 1.2
constraints     = h-bonds
pbc             = xyz

Preparing for Ionization:
gmx grompp -f ions_em.mdp -c solv.gro -p topol.top -o ions_NaCl.tpr -maxwarn 1

Ionization:
printf "SOL\n" | gmx genion -s ions_NaCl.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -neutral -conc 0.15

Minimize and equilibrate

em.mdp / nvt.mdp / npt.mdp with CHARMM36m defaults

gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr
gmx mdrun -deffnm em

gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr
gmx mdrun -deffnm nvt

gmx grompp -f npt.mdp -c nvt.gro -p topol.top -o npt.tpr
gmx mdrun -deffnm npt

Production

md.mdp (100 ns)

gmx grompp -f md.mdp -c npt.gro -p topol.top -o md.tpr
gmx mdrun -deffnm md

Citations

  • AlphaFold3: Abramson, J. et al. AlphaFold 3. Nature (2024).
  • MD Analysis: Lemkul, J.A. From Proteins to Perturbed Hamiltonians...
  • Chemokine heterodimers: Kaffashi, K.; Dréau, D.; Nesmelova, I.V. Heterodimers Are an Integral Component of Chemokine Signaling Repertoire. Int. J. Mol. Sci. 2023.