Module: Precompute Alignment ()

Description:

This module can be used to generate a data object that contains an alignment for every step of a whole Molecule Trajectory.

Press the Apply button to start the computation.

Connections:

Data [required]
The molecule must be connected to the Molecule Trajectory molecular dynamics trajectory that the alignment should be computed for.

AlignMaster [optional]
Reference molecule.

PrecomputedAlignment [optional]
You will find the description of the above two connections in the section on alignment of molecules.

Ports:

Mode

Two modes are available. In the first mode (simple alignment), the module acts as a recorder for the time-step-based alignments described in the section Aligning Molecules. In the second mode (multiple alignment), the mean squared distance of every time step to all other time steps is minimized. A reference molecule can be connected to specify atoms to be taken into account. If a reference is connected, the mean of the aligned time steps will be aligned to the reference.

Alignment



You will find the description of the three ports above in the section on alignment of molecules.