PUCKERING

This is part of the colvar module

Calculate the Nucleic Acid sugar pseudorotation coordinates.

This command can be used to represent the ring's pseudorotation with polar coordinates (Phase, Amplitud) or cartesian coordinates (Zx, Zy) using the position of the five ring atoms ( see [25] ).

Components of this action are:

Description of components

By default this Action calculates the following quantities. These quanties can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the quantity required from the list below.

Quantity	Description
phs	Pseudorotaion phase
amp	Pseudorotation amplitude
Zx	Pseudorotation x cartesian component
Zy	Pseudorotation y cartesian component

The atoms involved can be specified using

ATOMS

the five atoms of the sugar ring in the order C4',O4',C1',C2',C3'. For more information on how to specify lists of atoms see Groups and Virtual Atoms

Options

NUMERICAL_DERIVATIVES

( default=off ) calculate the derivatives for these quantities numerically

Examples

This input tells plumed to print the puckering phase angle of the 3rd nucleotide of a RNA molecule on file COLVAR.

 MOLINFO STRUCTURE=rna.pdb MOLTYPE=rna
 PUCKERING ATOMS=@sugar-3 LABEL=puck
 PRINT ARG=puck.phs FILE=COLVAR