CV:ACYL

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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 acylindricity of atom distribution in the group A. The value is zero when the distribution of atoms is cylindrically symmetric.

$\xi = \lambda_y^2 - \lambda_x^2$

where λ are principal moments of the gyration tensor. 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: ACYL

Key	Type	Default	Description
name	string		unique CV name
group_a	mask		atoms specifying the group A

Keys in bold are mandatory.