The AveragePos command calculates and sets the final average atom positions using the data accumulated before with the AddPos command.

The complete procedure for calculating average positions is as follows (and implemented as part of the macro md_analyze):

• Load the starting structure as a reference.
• Load a simulation snapshot.
• Superpose it onto the reference structure to remove translational and rotational degrees of freedom.
• Use AddPos to add the current atom positions to the internal calculation table.
• Repeat for all simulation snapshots.
• In the end, use AveragePos to move the atoms to their average positions

Use the Clear command to clear the internal atom position table and start a new round of calculations.

AveragePosAtom Obj 1

Move each atom in object 1 to its average positions.

AveragePosRes Obj 1

Move each atom in object 1 to the average position if its residue. This will collapse all residues to single points.