Collective Variables

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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

Collective variables (CVs) define a subset of configuration space in which free energy is being calculated.

The CV definition can be read either from the input file or from an external file. The mode will depend on configuration in the [files] section. If the value of the fcvsdef key contains the name of the group (e.g. string starting with the "{" character) then the CV definition will be read from this group in the input file. Otherwise, the CV definition will be read from a file with the name provided by the fcvsdef key. In the latter case, the CV definition must be in the {MAIN} group (which is implicit and can be omitted in the file).

The group or file can contain several collective variables. Each collective variable is specified in a single section. The name of the section defines a type of CV. The section contains the name key containing a unique CV name and other keys specific to a given CV type.

Extra documentation:

• Nucleic Acids
• Ring Puckering
• Macrocycle Threading

Supported Types

Distance
Type	Description	Type	Description
DD	distance difference	DIS	distance between two points
MDIS	minimum value of atom pair distances	MDISG	minimum distance between two atom groups
ODIS	distance between plane and point	OPOS	absolute position in the oriented coordinate system
ORAD	radial distance in the oriented coordinate system	POS	absolute position
RAD	radial distance
Angle
Type	Description	Type	Description
ANG	angle among three points	ANG2	angle between two vectors defined by four points
AXANG	angle between two principal axes	AXANG2	angle between two reference axes
DIH	dihedral angle among four points	DIH2	dihedral angle among three vectors defined by six points
PANG	angle between two planes	PVANG	angle between plane and vector
Coordination Numbers
Type	Description	Type	Description
CNFF	coordination number atom-atom using Fermi like function	CNGFF	coordination number point-atom using Fermi like function
CNSW	coordination number atom-atom using switch function	CNGSW	coordination number point-atom using switch function
CNRF	coordination number atom-atom using rational function	CNGRF	coordination number point-atom using rational function
Shape
Type	Description	Type	Description
ACYL	acylindricity	PMGTD	difference of two principal moments of gyration tensor
ASPH	asphericity	PMOGT	principal moment of gyration tensor
SANIS	relative shape anisotropy	RMSDT	root-mean square deviation to target structure
RGYR	radius of gyration	PLANE	root-mean-square deviation from the plane
EVEC	projection into essential vector
Nucleic Acids
Type	Description	Type	Description
NALBPP	local base-pair parameters	NALSTP	local base-pair step parameters
NASBPP	simple base-pair parameters	NASSTP	simple base-pair step parameters
NASBPPOLD	simple base-pair parameters	NASSTPOLD	simple base-pair step parameters
NASBO	simple base-pair opening	NAPBO	primitive base-pair opening
NABEND	nucleic acid bending
Ring Puckering
Type	Description	Type	Description
PUCK6Q	total puckering amplitude of six-membered ring	PUCK5Q	total puckering amplitude of five-membered ring
PUCK6P	puckering azimuthal angle of the six-membered ring	PUCK5P	puckering azimuthal angle of the five-membered ring
PUCK6T	puckering polar angle of the six-membered ring
Energy
Type	Description	Type	Description
POT	potential energy	EGAP	energy gap between two resonance states
Algebra
Type	Description	Type	Description
ADD	sum of two collective variables	SUB	difference between two collective variables
MULT	product of two collective variables	DIV	ratio of two collective variables
FSWITCH	Fermi-like switch function	RSWITCH	rational switch function