Nucleic Acids

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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

Implemented Collective Variables

Type	Description
NASBPP	simple base pair parameters
NABEND	nucleic acid bending
NAPBO	primitive base opening
NASBO	simple base opening

Simple Base Pair Parameters

All simple base pair parameters (i.e., shear, stretch, stagger, buckle, propeller, opening) fully compatible with 3DNA are available via NASBPP.

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Reference coordinates for nucleobase rings are available here:

Nucleobase	anti	syn
A
G
C
T

References

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