CV:PANG

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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 normal plane vectors.

$\xi =arccos({\mathbf{𝐧}}_A.{\mathbf{𝐧}}_B)$

The planes are defined as the best fit among atoms in each atom group. The fit is mass weighted.

$\psi ({\mathbf{𝐧}}_A^{\text{'}})=\sum _{i=1}^{grou{p}_A}{m}_i[{\mathbf{𝐧}}_A^{\text{'}}.({\mathbf{𝐱}}_i-{\mathbf{𝐀}}_{com}){]}^2\to min!$ $\psi ({\mathbf{𝐧}}_B^{\text{'}})=\sum _{i=1}^{grou{p}_B}{m}_i[{\mathbf{𝐧}}_B^{\text{'}}.({\mathbf{𝐱}}_i-{\mathbf{𝐁}}_{com}){]}^2\to min!$

The orientation of the plane normal vectors is controled by two helper vectors x_dir and y_dir:

${\mathbf{𝐧}}_A=sign({\mathbf{𝐧}}_A^{\text{'}}.({\mathbf{𝐱}}_{dir,a}\times {\mathbf{𝐲}}_{dir,a})){\mathbf{𝐧}}_A^{\text{'}}$ ${\mathbf{𝐧}}_B=sign({\mathbf{𝐧}}_B^{\text{'}}.({\mathbf{𝐱}}_{dir,b}\times {\mathbf{𝐲}}_{dir,b})){\mathbf{𝐧}}_B^{\text{'}}$

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

Specification

Section name: PANG

Key	Type	Default	Description
name	string		unique CV name
group_a	mask		atoms specifying the plane A
x_direction_a	mask		single atom specifying the end of approximate x-direction vector. The vector origin is in Acom. The atom must be member of the group A.
y_direction_a	mask		single atom specifying the end of approximate y-direction vector. The vector origin is in Acom. The atom must be member of the group A.
group_b	mask		atoms specifying the plane B
x_direction_b	mask		single atom specifying the end of approximate x-direction vector. The vector origin is in Bcom. The atom must be member of the group B.
y_direction_b	mask		single atom specifying the end of approximate y-direction vector. The vector origin is in Bcom. The atom must be member of the group B.

Keys in bold are mandatory.