CV:OPOS2

Navigation: Documentation / Collective Variables / CV:ORAD

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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 radial distance of the point from z-axis of re-oriented coordinate system along principal moments of the tensor inertia I.

$\xi = \sqrt{{A'}_{com,x}^2 + {A'}_{com,y}^2}$

The z-axis can be reoriented to any axis of the re-oriented coordinate system.

The relation between re-oriented (') and native coordinate system is given by the transformation matrix T:

Failed to parse (Conversion error. Server ("cli") reported: "[INVALID]"): {\displaystyle \bold A_{com}^' = \bold T \bold A_{com}}

Specification

Section name: ORAD

Key	Type	Default	Description
name	string		unique CV name
group_a	mask		atoms specifying the point A
z_direction	mask		single atom specifying the end of approximate z-direction vector of the re-oriented coordinate system. The vector origin is in Acom. The atom must be member of the group A.
direction	x, y, z		determine direction of z-axis in the re-oriented coordinate system

Keys in bold are mandatory.