CV:NASBPP

Navigation: Documentation / Collective Variables / CV:NASBPP

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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 simple base pair parameters for the A:B base pair.

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

Specification

Section name: NASBPP

Key	Type	Default	Description
name	string		unique CV name
group_a	mask		atoms for the base A ring 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
direction_a	x, y, z		selection of corresponding axis of the reference frame 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
direction_b	x, y, z		selection of corresponding axis of the reference frame B

Keys in bold are mandatory.