CV:WORMPOS

Navigation: Documentation / Collective Variables / Macrocycle Threading / CV:WORMPOS

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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 parametric position of an axle (guest) inside a macrocycle (host), for further details, see Macrocycle Threading.

Specification

Section name: WORMPOS

Key	Type	Default	Description
name	string		unique CV name
group_a	mask		atoms specifying the plane representing a host (H)
x_direction	mask		single atom specifying the end of approximate x-direction vector. The vector origin is in Hcom. The atom must be a member of the group_a.
y_direction	mask		single atom specifying the end of approximate y-direction vector. The vector origin is in Hcom. The atom must be a member of the group_a.
seldist	real		the size of a selector zone
steepness	real		steepness of the selector boundary
nsegs	integer		number of control points representing a guest
totlen	real		sum of distances between control points
alpha_x	real		parametric position of given control point (alpha_a, alpha_b, etc.)
fragment_x	mask		COM of given control point (fragment_a, fragment_b, etc.)

Keys in bold are mandatory.