6.1.2. Dihedral Analysis¶
Analyzes selected dihedral angles over a multi-system
simulation. Built using the framwework to run over a collection
of systems contained in an Ensemble
.
New in version 0.8.0.
-
class
mdpow.analysis.dihedral.
DihedralAnalysis
(dihedral_groups: List[mdpow.analysis.ensemble.EnsembleAtomGroup])[source]¶ Analyzes dihedral angles of selections from a single
Ensemble
.Keywords: - dihedral_groups
- list of
EnsembleAtomGroup
with four atoms selected on each. All selections must be from the sameEnsemble
.
Data is returned in a
pandas.DataFrame
with observations sorted by selection, solvent, interaction, lambda, time.Example
Typical Workflow:
ens = Ensemble(dirname='Mol') dihedral1 = Ens.select_atoms('name C1 or name C2 or name C3 or name C4') dihedral2 = Ens.select_atoms('name C5 or name C8 or name C10 or name C12') dih_run = DihedralAnalysis([dihedral1, dihedral2]).run(start=0, stop=10, step=1)
-
run
(start=None, stop=None, step=None)¶ Runs
_single_universe()
on each system or_single_frame()
on each frame in the system.First iterates through keys of ensemble, then runs
_single_universe()
or_single_frame()
.