CV:ODIS

Navigation: Documentation / Collective variables / CV:ODIS

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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 oriented distance between the plane A and the point B.

$\xi = sign( \bold n_A . (\bold x_{dir} \times \bold y_{dir}) ) [\bold n_A .( \bold B_{com} - \bold A_{com})]$

where n_A is the plane normal vector. x_dir and y_dir are helper vectors defining the plane orientation and thus avoid flipping of colective variable sign due to ambitious orientation of the plane normal vector.

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

$\psi(\bold n_A) = \sum_{i=1}^{group_A}{m_i[\bold n_A .( \bold x_i - \bold A_{com})]^2} \rightarrow min!$

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

Specification

Section name: ODIS

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

Keys in bold are mandatory.