Gro: set of classes to handle Gromacs input and output data

Classes

GMolecule

Represents an individual molecule.

• Z: atomic numbers;
• xyz: coordinates in Å;
• name: short name of the compound. Typically, for Gromacs studied species is LIG, and solvent is SOL (water can be WAT as well);
• index: unique index of the molecule.

GFrame

Represents an individual snapshot from MD simulation, i.e., a collection of GMolecules. Can handle a single *.gro file (which can be an input for a simulation run as well as an output).

GTrajectory

Represents a MD trajectory, i.e. a collection of GFrames. Can handle raw binary *.trr file and also ASCII *.gro file.

Features

• Automatically fixes the molecules at the edge of the simulation box. Typically raw output from Gromacs contains 'broken' molecules, e.g. some atoms are on another side of the box than the others. Currently fix() is called for each molecule which makes reading of large TRR files rather slow. To be optimized.
• Deduces the local neighbourhood for selected molecules. This is used to generate an input for e.g. spectral calculations, which require only a small blob of atoms.
• Removes virtual atoms, used by some MD simulations E.g. widely used TIP4P model of water consists of 4 atoms (O, H, H and one virtual).

Examples

Individual gromacs snapshot

# read individual snapshot
filename = 'md.gro'
gro = GFrame(filename)

# molecule in the frame
print(gro.n_molecules_)

# xyz array
print(gro.xyz)

# get neighbourhood for a given molecule
## the following code returns the system of all the molecules, whoch are neighbours of molecule #10
## neighbours are the molecules such that all atoms are within given distance threshold from the target
## resulting system is centered at atom #6 of the molecule #10 (convenient for visualization or spectral
## calculations)
nei = gro.neighbourhood(10, dist={'SOL': 5, 'LIG': 7.5}, center_at=6)
nei.to_xyz() # prints the content of the system
nei.to_xyz(filename=<>) # saves .xyz file

Trajectory (requires also gro file, since trajectorry file containes only coordinates, timing, box size, but not atomic numbers)

file_trr = 'md.trr'
file_gro = 'md.gro'
traj = GTrajectory(file_trr, file_gro)  # takes a while to read binary data and also fix the molecules
gro = traj[0]  # get the first frame of the trajectory