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 / Path

PTPATHS, PTPATHS2P, PTPATHS2PN, PTPATHZ, PATHS2, PATHZ, WORMPOS, WORMANG

Energy

POT

Algebra

ADD, SUB, MULT, DIV, FSWITCH, RSWITCH

Collective variables (CVs) define a reduced subset of the configurational space in which free-energy calculations are performed.

The CV definition can be provided either directly in the input file or in an external file. The selected mode depends on the configuration in the [files] section.

If the value of the fcvsdef key specifies the name of an input-file group, for example a string beginning with the "{" character, the CV definition is read from this group in the input file. Otherwise, the value of fcvsdef is interpreted as the name of an external file containing the CV definition. In this case, the CV definition must be placed in the {MAIN} group, which is implicit and may be omitted from the file.

A single group or file may define multiple collective variables. Each collective variable is specified in a separate section. The section name determines the CV type. Each section must contain the name key, which defines a unique name of the CV, together with additional keys specific to the selected 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 atom-pair distance	MDISG	minimum distance between two atom groups
ODIS	distance between a plane and a point
OPOS	absolute position in an oriented coordinate system	OPOS2	absolute position in a superimposed coordinate system
ORAD	radial distance in an oriented coordinate system	ORAD2	radial distance in a superimposed coordinate system
POS	absolute position	RAD	radial distance
Angle
Type	Description	Type	Description
ANG	angle defined by 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 defined by four points	DIH2	dihedral angle defined by three vectors and six points
PANG	angle between two planes	PVANG	angle between a plane and a vector
Coordination Numbers
Type	Description	Type	Description
CNFF	atom-atom coordination number calculated using a Fermi-like function	CNGFF	point-atom coordination number calculated using a Fermi-like function
CNSW	atom-atom coordination number calculated using a switching function	CNGSW	point-atom coordination number calculated using a switching function
CNRF	atom-atom coordination number calculated using a rational function	CNGRF	point-atom coordination number calculated using a rational function
Shape
Type	Description	Type	Description
ACYL	acylindricity	PMGTD	difference between two principal moments of the gyration tensor
ASPH	asphericity	PMOGT	principal moment of the gyration tensor
SANIS	relative shape anisotropy	RMSDT	root-mean-square deviation from a target structure
RGYR	radius of gyration	PLANE	root-mean-square deviation from a plane
EVEC	projection onto an 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	legacy simple base-pair parameters	NASSTPOLD	legacy 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 a six-membered ring	PUCK5Q	total puckering amplitude of a five-membered ring
PUCK6P	puckering azimuthal angle of a six-membered ring	PUCK5P	puckering azimuthal angle of a five-membered ring
PUCK6T	puckering polar angle of a six-membered ring
Special / Path
Type	Description	Type	Description
PTPATHS	path-progress coordinate for point-based paths	PTPATHS2P	two-point path-progress coordinate for point-based paths
PTPATHS2PN	normalized two-point path-progress coordinate for point-based paths	PTPATHZ	path-distance coordinate for point-based paths
PATHS	path-progress coordinate	PATHZ	path-distance coordinate
WORMPOS	parametric position of an axle inside a macrocycle	WORMANG	orientation of an axle inside a macrocycle
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 switching function	RSWITCH	rational switching function