a3fe.analyse.rmsd
Functionality to compute RMSDs
Functions
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Return the RMSD for a given MDAnalysis selection. |
- a3fe.analyse.rmsd.get_rmsd(input_dirs: List[str], selection: str, tot_simtime: float, reference_traj: str, group_selection: str | None = None) Tuple[ndarray, ndarray][source]
Return the RMSD for a given MDAnalysis selection. Reference frame taken as the first frame, regardless of whether the total equilibration time is 0 or not.
Note that if group_selection is None, the same selection as the one used for the RMSD calculation will be used, otherwise the group_selection will be used for the RMSD calculation.
- Parameters:
input_dirs (List[str]) – List of absolute paths to the output directories containing the trajectory information and the topology files.
selection (str) – The selection, written using the MDAnalysis selection language, to use for the calculation of RMSD.
tot_simtime (float) – The total simulation time per simulation.
reference_traj (str) – The absolute path to the reference trajectory file. The reference will be taken as the first frame of this trajectory.
group_selection (Optional[str], default=None) – The selection, written using the MDAnalysis selection language, to use for the calculation of RMSD, after the alignment of the trajectory according to the selection passed as “selection”. If None, the same selection as the one used for the RMSD calculation will be used.
- Returns:
rmsds (_np.ndarray) – An array of the RMSDs, in nm, for each simulation with reference to the first frame of the reference trajectory.
times (_np.ndarray) – An array of the times, in ns, corresponding to the RMSDs