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Gromacs

Guide to preparing Gromacs trajectories for upload to NOMAD

Options 1 to 3 rely only on Gromacs on-board tools: gmx trjconv, gmx editconv, and gmx make_ndx. Option 4 uses MDAnalysis to process the trajectory.

1. Reduce the number of frames in the trajectory

Specify which time steps to keep by only copying every n-th frame:

  • gmx trjconv -f [<.xtc/.trr/...>] -dt n -o [<.xtc/.trr/...>]

2. Remove solvent from the trajectory file using Gromacs tools

WARNING: May not work if more than one solute type need to be retained!!!

(E.g. a complex of two different molecules.)

  • Specify elements in your system to retain in the index file: gmx make_ndx -f original.tpr -o modified.ndx
  • Remove all other parts of the system from the trajectory: gmx trjconv -f original.xtc -o modified.xtc -n modified.ndx
  • Remove all other parts of the system from the *.gro file: gmx editconf -f original.gro -o modified.gro -n modified.ndx
  • Remove all other parts of the system from the *.tpr file: gmx convert-tpr -s original.tpr -o modified.tpr -n modified.ndx

3. Manually remove solvent from the trajectory

  • Manually delete solvent entries from *.top file using a text editor:

  • Remove solvent entry under [ molecules ].

  • (Optional: Remove solvent topology by deleting the corresponding sections or #include solvent.itp statements.)

  • The name of the [ moleculetype ] in the *.top file defines the name of the system component in the NOMAD entry!

  • Adjust *.mdp file

    • Remove solvent group(s) for temperature (pressure) coupling. Group names must match either [moleculetype] names or custom index group names.
  • Manually delete solvent entries from index file:
    • Remove solvent indices from [ system ].
    • Remove solvent indices from [ other ].
    • Remove section corresponding to your solvent.
    • (Optional: remove indices and sections corresponding to ions.)
  • Generate new *.gro file: gmx editconf -f original.gro -o modified.gro -n modified.ndx
  • Generate new *.tpr file from edited *.top and *.mdp files: gmx grompp -f modified.mdp -c modified.gro -p modified.top -o modified.tpr
  • Remove all other parts of the system from the trajectory: gmx trjconv -f original.xtc -o modified.xtc -n modified.ndx

4. Use MDAnalysis to modify your trajectory and remove solvent

import MDAnalysis as mda

# Set up trajectory and topology files and locations for the conversion

dir_path = '/path/to/original/gromacs/files' # Path to the directory containing the trajectory and topology files
top_file = f'{dir_path}/<original>.tpr' # Topology file
traj_file = f'{dir_path}/<original>.xtc' # Trajectory file
new_name = '<modified>' # Name for the modified trajectory
solvent = 'SOL' # Name of your solvent you want to remove (resname)
mol_name = 'POL' # Name of one molecule you want to retain (resname)
lig_name = 'LIG' # Name of a second molecule you want to retain (resname)

# Load the trajectory and topology files as a MDAnalysis Universe object
u = mda.Universe(top_file, traj_file)

# MDAnalysis allows full control over the components of the system that are selected:
# https://docs.mdanalysis.org/stable/documentation_pages/selections.html
# https://userguide.mdanalysis.org/stable/selections.html

# Example: Select all system components that are not the solvent
solutes = u.select_atoms(f'not resname {solvent}')

# Write a new trajectory where each frame only contains the solute molecules
with mda.Writer(f'{dir_path}/{new_name}.xtc', n_atoms=solutes.n_atoms) as w:
    for ts in u.trajectory[:]: # Using the python slicing operator [start:stop:step], the number of frames can be reduced at this point
        w.write(solutes)

# Write a new gro file containing only the solute molecules
with mda.Writer(f'{dir_path}/{new_name}.gro') as w:
    w.write(solutes.atoms)

# Optional: Write a new index file containing only the solute molecules:

# If multiple individual solute groups are needed, they need to be individually written to the index file.
with mda.selections.gromacs.SelectionWriter(f'{dir_path}/{new_name}.ndx', mode='w') as ndx:
    ndx.write(u.select_atoms(f'resname {mol_name}'), name=f'{mol_name}')
    ndx.write(u.select_atoms(f'resname {lig_name}'), name=f'{lig_name}')
  • Adjust *.mdp file using a text editor:
  • Remove solvent group(s) for temperature (pressure) coupling.
  • Manually delete solvent entries from *.top file using a text editor:
  • Remove solvent entry under [molecules] in the [system] section at the end of the *.top file.
  • The name of the [ moleculetype ] in the *.top file defines the name of the system component in the NOMAD entry.
  • Generate new *.tpr file from edited *.top, *.mdp and *.gro files: gmx grompp -f modified.mdp -c modified.gro -p modified.top -o modified.tpr
  • (Optional: An updated *.tpr file can be written in a script using GromacsWrapper)