CV:AXANG2

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Distance

DD, DIS, MDIS, MDISG, ODIS, OPOS, OPOS2, ORAD, ORAD2, POS, RAD

Angle

ANG, ANG2, AXANG, AXANG2, DIH, DIH2, PANG, PVANG

Coordination

CNFF, CNGFF, CNSW, CNGSW, CNRF, CNGRF

Shape

ACYL, ASPH, EVEC, PMGTD, PMOGT, PLANE, RGYR, RMSDT, SANIS

Nucleic Acids

NALBPP, NASBPP, NASBPPOLD, NALSTP, NASSTP, NASSTPOLD, NASBO, NAPBO, NABEND

Puckering

PUCK6Q, PUCK6P, PUCK6T, PUCK5Q, PUCK5P

Special

WORMPOS, WORMANG

Energy

POT, EGAP

Algebra

ADD, SUB, MULT, DIV, FSWITCH, RSWITCH

Definition

The angle between two axes of two reference frames superimposed to the atom groups A and B.

$\xi = arccos \left( \bold n_A . \bold n_B \right)$

The superimposition is made by finding lowest root mean square deviation between the reference structure and structure of a given atom group. The fit is not mass weighted.

Failed to parse (Conversion error. Server ("cli") reported: "[INVALID]"): {\displaystyle RMSD = \sqrt{ {\sum_{i=1}^{N}{ | \bold R_i^' - \bold R_{ref,i}|^2 }} } \rightarrow min!}

where R^' are atoms from given atom group and R_ref are atoms from given reference structure.

PBC note: The minimum-image convention is not used.

Specification

Section name: AXANG

Key	Type	Default	Description
name	string		unique CV name
group_a	mask		atoms employed in the superimposition of the reference frame a
reference_a	string		name of file with the reference structure in the XYZ format, the structure must have the same number of atoms as the group group_a
direction_a	x, y, z		selection of corresponding axis of the reference frame a
group_b	mask		atoms employed in the superimposition of the reference frame b
reference_b	string		name of file with the reference structure in the XYZ format, the structure must have the same number of atoms as the group group_b
direction_b	x, y, z		selection of corresponding axis of the reference frame b

Keys in bold are mandatory.