Getting root-mean-square fluctuations

Computing per-atom RMSF values in nanometers over an aligned trajectory.

API documentation

See molsysmt.structure.get_rmsf().

import molsysmt as msm
trajectory = msm.systems['pentalanine']['traj_pentalanine.h5msm']
rmsf = msm.structure.get_rmsf(
    trajectory, selection='backbone', heavy_mode='force'
)
rmsf.shape

RMSF measures fluctuations around each atom’s mean position. Align frames first when global rotation or translation is not part of the motion you want to measure. The chunked reducer uses a streaming variance calculation and agrees with eager execution.