CV:NAPBO

Navigation: Documentation / Collective Variables / Nucleic Acids / CV:NAPBO

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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

Primitive definition of base pair opening for the A:B base pair defined as a dihedral angle between three vectors: base A vector (C and D points), helical axis vector (A and B points), and base B vector (E and F points). This CV should provide the same value as CV:DIH2 but with the different order of atom groups.

PBC note: The minimum-image convention is applied to vectors |AB|, |CD|, and |EF| only if the fenable_pbc option is activated. The convention is not used to calculate the center of mass. It is therefore required that atoms within a group are either covalently bound or are part of complex that will not be separated or reimaged during a simulation.

Specification

Section name: NAPBO

Key	Type	Default	Description
name	string		unique CV name
group_a	mask		atoms specifying the point A
group_b	mask		atoms specifying the point B
group_c	mask		atoms specifying the point C
group_d	mask		atoms specifying the point D
group_e	mask		atoms specifying the point E
group_f	mask		atoms specifying the point F

Keys in bold are mandatory.