6.19. GROMOS11 trajectory reader — MDAnalysis.coordinates.TRC
Reads coordinates, timesteps and box-sizes from GROMOS11 TRC trajectories.
To load the trajectory into Universe,
you need to provide topology information using a topology file such as
a PDB:
import MDAnalysis as mda
u = mda.Universe("topology.pdb", ["md_1.trc.gz","md_2.trc.gz"],
continuous=True)
Note
The GROMOS trajectory format organizes its data in blocks. A block starts with a blockname in capital letters (example: POSITIONRED) and ends with a line containing only ‘’END’’. Only the TITLE-block at the beginning of each file is mandatory, others blocks can be chosen depending on the task.
The trajectory format as well as all permitted blocks and their data are documented in the GROMOS Manual Vol. 4, chapter 2 and 4. The manual can be downloaded here: https://gromos.net/gromos11_pdf_manuals/vol4.pdf
This reader is designed to read the blocks “TIMESTEP”, “POSITIONRED” and “GENBOX” from the trajectory which covers the standard trajectories of most simulations . If a trajectory includes other blocks, a warning is served and the blocks are ignored.
Note
MDAnalysis requires the blocks to be in the same order for each frame and ignores non-supported blocks.
6.19.1. Classes
- class MDAnalysis.coordinates.TRC.TRCReader(filename, convert_units=True, **kwargs)[source]
Coordinate reader for the GROMOS11 format
- property n_atoms
The number of atoms in one frame.
- property n_frames
The number of frames in the trajectory.
- units = {'length': 'nm', 'time': 'ps'}
dict with units of of time and length (and velocity, force, … for formats that support it)