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{{CVS}}__NOEDITSECTION__
{{CVS}}__NOEDITSECTION__


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


The CV definition can be read either from the input file or from an external file. The mode will depend on configuration in the [[General setup|[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 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 [[General setup|[files]]] section.


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.  
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:
Extra documentation:
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* [[Ring Puckering]]
* [[Ring Puckering]]
* [[Macrocycle Threading]]
* [[Macrocycle Threading]]
* [[CV:PTPATHS]]


===Supported Types===
===Supported Types===
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|-
|-
| [[CV:MDIS|MDIS]]
| [[CV:MDIS|MDIS]]
| minimum value of atom pair distances
| minimum atom-pair distance
| [[CV:MDISG|MDISG]]
| [[CV:MDISG|MDISG]]
| minimum distance between two atom groups
| minimum distance between two atom groups
|-
|-
| [[CV:ODIS|ODIS]]
| [[CV:ODIS|ODIS]]
| distance between plane and point
| distance between a plane and a point
|
|
|
|
|-
|-
| [[CV:OPOS|OPOS]]
| [[CV:OPOS|OPOS]]
| absolute position in the oriented coordinate system
| absolute position in an oriented coordinate system
| [[CV:OPOS2|OPOS2]]
| [[CV:OPOS2|OPOS2]]
| absolute position in the superimposed coordinate system
| absolute position in a superimposed coordinate system
|-
|-
| [[CV:ORAD|ORAD]]
| [[CV:ORAD|ORAD]]
| radial distance in the oriented coordinate system
| radial distance in an oriented coordinate system
| [[CV:ORAD2|ORAD2]]
| [[CV:ORAD2|ORAD2]]
| radial distance in the superimposed coordinate system
| radial distance in a superimposed coordinate system
|-
|-
| [[CV:POS|POS]]
| [[CV:POS|POS]]
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|-
|-
| [[CV:ANG|ANG]]
| [[CV:ANG|ANG]]
| angle among three points
| angle defined by three points
| [[CV:ANG2|ANG2]]
| [[CV:ANG2|ANG2]]
| angle between two vectors defined by four points
| angle between two vectors defined by four points
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|-
|-
| [[CV:DIH|DIH]]
| [[CV:DIH|DIH]]
| dihedral angle among four points
| dihedral angle defined by four points
| [[CV:DIH2|DIH2]]
| [[CV:DIH2|DIH2]]
| dihedral angle among three vectors defined by six points
| dihedral angle defined by three vectors and six points
|-
|-
| [[CV:PANG|PANG]]
| [[CV:PANG|PANG]]
| angle between two planes
| angle between two planes
| [[CV:PVANG|PVANG]]
| [[CV:PVANG|PVANG]]
| angle between plane and vector
| angle between a plane and a vector
|-
|-
| colspan="4" style="text-align: center; background-color: #CCCCFF;" | '''Coordination Numbers'''
| colspan="4" style="text-align: center; background-color: #CCCCFF;" | '''Coordination Numbers'''
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|- valign="top"
|- valign="top"
| [[CV:CNFF|CNFF]]
| [[CV:CNFF|CNFF]]
| coordination number atom-atom using Fermi like function
| atom-atom coordination number calculated using a Fermi-like function
| [[CV:CNGFF|CNGFF]]
| [[CV:CNGFF|CNGFF]]
| coordination number point-atom using Fermi like function
| point-atom coordination number calculated using a Fermi-like function
|- valign="top"
|- valign="top"
| [[CV:CNSW|CNSW]]
| [[CV:CNSW|CNSW]]
| coordination number atom-atom using switch function
| atom-atom coordination number calculated using a switching function
| [[CV:CNGSW|CNGSW]]
| [[CV:CNGSW|CNGSW]]
| coordination number point-atom using switch function
| point-atom coordination number calculated using a switching function
|- valign="top"
|- valign="top"
| [[CV:CNRF|CNRF]]
| [[CV:CNRF|CNRF]]
| coordination number atom-atom using rational function
| atom-atom coordination number calculated using a rational function
| [[CV:CNGRF|CNGRF]]
| [[CV:CNGRF|CNGRF]]
| coordination number point-atom using rational function
| point-atom coordination number calculated using a rational function
|-
|-
| colspan="4" style="text-align: center; background-color: #CCCCFF;" | '''Shape'''
| colspan="4" style="text-align: center; background-color: #CCCCFF;" | '''Shape'''
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| acylindricity
| acylindricity
| [[CV:PMGTD|PMGTD]]
| [[CV:PMGTD|PMGTD]]
| difference of two principal moments of gyration tensor
| difference between two principal moments of the gyration tensor
 
|-
|-
| [[CV:ASPH|ASPH]]
| [[CV:ASPH|ASPH]]
| asphericity
| asphericity
| [[CV:PMOGT|PMOGT]]
| [[CV:PMOGT|PMOGT]]
| principal moment of gyration tensor
| principal moment of the gyration tensor
|-
|-
| [[CV:SANIS|SANIS]]
| [[CV:SANIS|SANIS]]
| relative shape anisotropy
| relative shape anisotropy
| [[CV:RMSDT|RMSDT]]
| [[CV:RMSDT|RMSDT]]
| root-mean square deviation to target structure
| root-mean-square deviation from a target structure
|-
|-
| [[CV:RGYR|RGYR]]
| [[CV:RGYR|RGYR]]
| radius of gyration
| radius of gyration
| [[CV:PLANE|PLANE]]
| [[CV:PLANE|PLANE]]
| root-mean-square deviation from the plane
| root-mean-square deviation from a plane
|-
|-
| [[CV:EVEC|EVEC]]
| [[CV:EVEC|EVEC]]
| projection into essential vector
| projection onto an essential vector
|
|
|
|
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|-
|-
| [[CV:NASBPPOLD|NASBPPOLD]]
| [[CV:NASBPPOLD|NASBPPOLD]]
| simple base-pair parameters
| legacy simple base-pair parameters
| [[CV:NASSTPOLD|NASSTPOLD]]
| [[CV:NASSTPOLD|NASSTPOLD]]
| simple base-pair step parameters
| legacy simple base-pair step parameters
|-
|-
| [[CV:NASBO|NASBO]]
| [[CV:NASBO|NASBO]]
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|-
|-
| [[CV:NABEND|NABEND]]
| [[CV:NABEND|NABEND]]
| nucleic acid bending  
| nucleic acid bending
<!--
<!--
|-
|-
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|-
|-
| [[CV:ALPHA|ALPHA]]
| [[CV:ALPHA|ALPHA]]
| content of the alpha-helix structure
| alpha-helix content
| [[CV:PBETA|PBETA]]
| [[CV:PBETA|PBETA]]
| content of the parallel beta-sheet structure
| parallel beta-sheet content
|-
|-
| [[CV:ABETA|ABETA]]
| [[CV:ABETA|ABETA]]
| content of the antiparallel beta-sheet structure
| antiparallel beta-sheet content
|
|
| -->
| -->
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|-
|-
| [[CV:PUCK6Q|PUCK6Q]]
| [[CV:PUCK6Q|PUCK6Q]]
| total puckering amplitude of six-membered ring
| total puckering amplitude of a six-membered ring
| [[CV:PUCK5Q|PUCK5Q]]
| [[CV:PUCK5Q|PUCK5Q]]
| total puckering amplitude of five-membered ring
| total puckering amplitude of a five-membered ring
 
|-
|-
| [[CV:PUCK6P|PUCK6P]]
| [[CV:PUCK6P|PUCK6P]]
| puckering azimuthal angle of the six-membered ring
| puckering azimuthal angle of a six-membered ring
| [[CV:PUCK5P|PUCK5P]]
| [[CV:PUCK5P|PUCK5P]]
| puckering azimuthal angle of the five-membered ring
| puckering azimuthal angle of a five-membered ring
|-
|-
| [[CV:PUCK6T|PUCK6T]]
| [[CV:PUCK6T|PUCK6T]]
| puckering polar angle of the six-membered ring
| puckering polar angle of a six-membered ring
|
|
|
|
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|-
|-
| [[CV:PTPATHS|PTPATHS]]
| [[CV:PTPATHS|PTPATHS]]
| test 1
| path-progress coordinate for point-based paths
| [[CV:PTPATHS2P|PTPATHS2P]]
| [[CV:PTPATHS2P|PTPATHS2P]]
| test 1
| two-point path-progress coordinate for point-based paths
|-
|-
| [[CV:PTPATHS2PN|PTPATHS2PN]]
| [[CV:PTPATHS2PN|PTPATHS2PN]]
| test 1
| normalized two-point path-progress coordinate for point-based paths
| [[CV:PTPATHZ|PTPATHZ]]
| [[CV:PTPATHZ|PTPATHZ]]
| test 1
| path-distance coordinate for point-based paths
|-
|-
| [[CV:PATHS|PATHS]]
| [[CV:PATHS|PATHS]]
| test 1
| path-progress coordinate
| [[CV:PATHZ|PATHZ]]
| [[CV:PATHZ|PATHZ]]
| test 1
| path-distance coordinate
|-
|-
| [[CV:WORMPOS|WORMPOS]]
| [[CV:WORMPOS|WORMPOS]]
| parametrical position of an axle inside a macrocycle
| parametric position of an axle inside a macrocycle
| [[CV:WORMANG|WORMANG]]
| [[CV:WORMANG|WORMANG]]
| orientation of an axle inside a macrocycle
| orientation of an axle inside a macrocycle
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|-
|-
| [[CV:FSWITCH|FSWITCH]]
| [[CV:FSWITCH|FSWITCH]]
| Fermi-like switch function
| Fermi-like switching function
| [[CV:RSWITCH|RSWITCH]]
| [[CV:RSWITCH|RSWITCH]]
| rational switch function
| rational switching function
|}
|}

Revision as of 20:07, 28 May 2026

Navigation: Documentation / Collective Variables

Distance

Angle

Coordination

Shape

Nucleic Acids

Puckering

Special / Path

Energy

POT

Algebra

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:

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 / Paths
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
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