CV:PLANE

Navigation: Documentation / Collective Variables / CV:PLANE

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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 root-mean square distance of atoms to the plane that is the best fit among them.

$\xi =\sqrt{\frac{\sum _{i=1}^{grou{p}_A}{m}_i({\mathbf{𝐧}}_A.[{\mathbf{𝐱}}_i-{\mathbf{𝐀}}_{com}]{)}^2}{\sum _{i=1}^{grou{p}_A}{m}_i}}$

where n_A is the plane normal vector.

The plane is defined as the best fit among atoms in the atom group A. The fit is mass weighted.

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

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

Specification

Section name: PLANE

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

Keys in bold are mandatory.