Advanced Features

Specialized options for complex systems and performance tuning. Use this page as a checklist; full CLI details stay in Running Molecular Dynamics.

Gaussian for Boron-Containing Molecules

  • Requires Gaussian. Only ligands/cofactors with boron trigger Gaussian optimization and charge calculation; others use the standard Antechamber path.

  • If Gaussian cannot be loaded, boron-containing molecules are skipped while other inputs continue.

  • Key flags: --activate_gaussian, --gaussian_exe, --gaussian_basis, --gaussian_memory.

  • Omit --activate_gaussian if Gaussian is already available on the node; use it only to run a load command such as module load Gaussian/09-d01.

run_md -p protein_H_HIS.pdb -l molecules.sdf --cofactor cofactors.sdf --md_time 1 \
  --activate_gaussian "module load Gaussian/09-d01" --gaussian_exe g09 --ncpu 128

MCPB.py for Metalloproteins

  • Also requires Gaussian. MCPB.py runs when metal residue names and Gaussian options are provided; otherwise StreaMD falls back to standard gmx2pdb.

  • Key flags: --metal_resnames, --metal_cutoff, --metal_charges plus Gaussian flags above.

run_md -p protein_H_HIS.pdb -l molecules.sdf --cofactor cofactors.sdf --md_time 1 \
  --activate_gaussian "module load Gaussian/09-d01" --gaussian_exe g09 --metal_resnames ZN

Custom MDP Files

  • Supply ions.mdp, minim.mdp, nvt.mdp, npt.mdp, or md.mdp via --mdp_dir. Missing files fall back to defaults.

  • StreaMD may override seed and timing if set via CLI; keep filenames unchanged for detection.

run_md -p protein.pdb -l ligand.mol --mdp_dir custom_mdp/ --md_time 5

Custom Force Field

Use any force field for pdb2gmx run available under your GROMACS installation (e.g., Miniconda3/envs/md/share/gromacs/top).

run_md -p protein_H_HIS.pdb --md_time 1 --protein_forcefield your_ff_name

The value passed to the --protein_forcefield option must match the directory name of the desired .ff package without the .ff extension.

StreaMD Step Control

  • --steps runs selected pipeline stages when continuing existing runs (1 preparation, 2 equilibration, 3 production, 4 analysis).

run_md --wdir_to_continue md_files/md_run/protein_H_HIS_ligand_1 --md_time 3 --steps 3 4

Trajectory Size and Diagnostics

  • --save_traj_without_water writes water-stripped trajectories for lighter analysis.

  • --no_dr skips acdoctor ligand diagnostics (use with care).

  • --deffnm sets a custom prefix for continuing/extending runs.

Parallelism and GPUs

  • Combine --device, --gpu_ids, --ntmpi_per_gpu, and --mdrun_per_node to balance CPU/GPU use; see examples in Running Molecular Dynamics.

  • Set the --ncpu option to limit CPU usage; by default, StreaMD uses all available CPU cores.

  • Distributed runs use --hostfile for Dask servers (PBS/SLURM examples in Running Molecular Dynamics).