CV:NABEND

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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

This CV provides dihedral angle between three vectors. Two vectors are defined as z-axes of two reference frames superimposed to the atom groups A and B, see CV:AXANG2, and the hinge vector is defined by difference between two COMs calculated from groups C and D.

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

Specification

Section name: NABEND

Key	Type	Default	Description
name	string		unique CV name
group_a	mask		atoms employed in the superimposition of the reference frame A
reference_a	string		name of file with the reference structure in the XYZ format, the structure must have the same number of atoms as the group group_a
group_b	mask		atoms employed in the superimposition of the reference frame B
reference_b	string		name of file with the reference structure in the XYZ format, the structure must have the same number of atoms as the group group_b
group_c	mask		atoms specifying the point C
group_d	mask		atoms specifying the point D

Keys in bold are mandatory.