# GromacsGroFile¶

class simtk.openmm.app.gromacsgrofile.GromacsGroFile(file)

GromacsGroFile parses a Gromacs .gro file and constructs a set of atom positions from it.

A .gro file also contains some topological information, such as elements and residue names, but not enough to construct a full Topology object. This information is recorded and stored in the object’s public fields.

__init__(file)

The atom positions can be retrieved by calling getPositions().

Parameters: file (string) – the name of the file to load

Methods

 __init__(file) Load a .gro file. getNumFrames() Get the number of frames stored in the file. getPeriodicBoxVectors([frame]) Get the vectors defining the periodic box. getPositions([asNumpy, frame]) Get the atomic positions. getUnitCellDimensions([frame]) Get the dimensions of the crystallographic unit cell.
getNumFrames()

Get the number of frames stored in the file.

getPositions(asNumpy=False, frame=0)

Get the atomic positions.

Parameters: asNumpy (boolean=False) – if true, the values are returned as a numpy array instead of a list of Vec3s frame (int=0) – the index of the frame for which to get positions
getPeriodicBoxVectors(frame=0)

Get the vectors defining the periodic box.

Parameters: frame (int=0) – the index of the frame for which to get the box vectors
getUnitCellDimensions(frame=0)

Get the dimensions of the crystallographic unit cell.

Parameters: frame (int=0) – the index of the frame for which to get the unit cell dimensions