CV:AXANG

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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 principal moments of the gyration tensor.

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

The mass weighted gyration tensor S is defined as

$S_{mn} \ = \frac {\sum_{i=1}^{N} m_i (x_{m}^{(i)} - x_{m}^{(\bold A)}) (x_{n}^{(i)} - x_{n}^{(\bold A)})}{\sum_{i=1}^{N} m_i}$

The eigenvalues of the tensor are $\lambda_{x}^2 \leq \lambda_{y}^2 \leq \lambda_{z}^2$:

$\bold S = \begin{bmatrix} \lambda_{x}^{2} & 0 & 0 \\ 0 & \lambda_{y}^{2} & 0 \\ 0 & 0 & \lambda_{z}^{2} \end{bmatrix}$

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 specifying the axis A
head_a	mask		single atom specifying the end of approximate vector in the direction of principal moment. The vector origin is in Acom. The atom must be member of the group A.
direction_a	x, y, z		select corresponding principal moment vector
group_b	mask		atoms specifying the axis B
head_b	mask		single atom specifying the end of approximate vector in the direction of principal moment. The vector origin is in Bcom. The atom must be member of the group B.
direction_b	x, y, z		select corresponding principal moment vector

Keys in bold are mandatory.