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


Collective variables (CVs) define subset of configuration space in which the free energy is being calculated.
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 [[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 later 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 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 group or file can contain several collective variables. Each collective variable is specified in a single section. The name of section defines type of CV. The section contains the name key containing a unique CV name and other keys specific for a given CV type.  
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===
===Supported Types===
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| [[CV:ODIS|ODIS]]
| [[CV:ODIS|ODIS]]
| distance between plane and point
| distance between plane and point
|
|
|-
| [[CV:OPOS|OPOS]]
| [[CV:OPOS|OPOS]]
| absolute position in oriented coordinate system
| absolute position in the oriented coordinate system
| [[CV:OPOS2|OPOS2]]
| absolute position in the superimposed coordinate system
|-
|-
| [[CV:ORAD|ORAD]]
| [[CV:ORAD|ORAD]]
| radial distance in oriented coordinate system
| radial distance in the oriented coordinate system
| [[CV:ORAD2|ORAD2]]
| radial distance in the superimposed coordinate system
|-
| [[CV:POS|POS]]
| [[CV:POS|POS]]
| absolute position
| absolute position
|-
| [[CV:RAD|RAD]]
| [[CV:RAD|RAD]]
| radial distance
| radial distance
|
|
|-
|-
| colspan="4" style="text-align: center; background-color: #CCCCFF;" | '''Angle'''
| colspan="4" style="text-align: center; background-color: #CCCCFF;" | '''Angle'''
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|-
|-
| [[CV:AXANG|AXANG]]
| [[CV:AXANG|AXANG]]
| angle between two axes
| angle between two principal axes
| [[CV:AXANG2|AXANG2]]
| angle between two reference axes
|-
| [[CV:DIH|DIH]]
| [[CV:DIH|DIH]]
| dihedral angle among four points
| dihedral angle among four points
| [[CV:DIH2|DIH2]]
| dihedral angle among three vectors defined by six points
|-
|-
| [[CV:PANG|PANG]]
| [[CV:PANG|PANG]]
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| radius of gyration
| radius of gyration
| [[CV:PLANE|PLANE]]
| [[CV:PLANE|PLANE]]
| root-mean square deviation from plane
| root-mean-square deviation from the plane
|-
|-
| [[CV:EVEC|EVEC]]
| [[CV:EVEC|EVEC]]
| projection into esential vector
| projection into essential vector
|
|
|
|
|-
|-
| colspan="4" style="text-align: center; background-color: #CCCCFF;" | '''Nucleic Acids'''
| colspan="4" style="text-align: center; background-color: #CCCCFF;" | '''[[Nucleic Acids]]'''
|-
|-
| style="width: 5em;" | '''Type'''
| style="width: 5em;" | '''Type'''
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| '''Description'''
| '''Description'''
|-
|-
| [[CV:NABO|NABO]]
| [[CV:NALBPP|NALBPP]]
| base opening
| local base-pair parameters
|  
| [[CV:NALSTP|NALSTP]]
|  
| local base-pair step parameters
|-
| [[CV:NASBPP|NASBPP]]
| simple base-pair parameters
| [[CV:NASSTP|NASSTP]]
| simple base-pair step parameters
|-
| [[CV:NASBPPOLD|NASBPPOLD]]
| simple base-pair parameters
| [[CV:NASSTPOLD|NASSTPOLD]]
| simple base-pair step parameters
|-
| [[CV:NASBO|NASBO]]
| simple base-pair opening
| [[CV:NAPBO|NAPBO]]
| primitive base-pair opening
|-
| [[CV:NABEND|NABEND]]
| nucleic acid bending
<!--
|-
| colspan="4" style="text-align: center; background-color: #CCCCFF;" | '''[[Peptides]]'''
|-
| style="width: 5em;" | '''Type'''
| '''Description'''
| style="width: 5em;" | '''Type'''
| '''Description'''
|-
| [[CV:ALPHA|ALPHA]]
| content of the alpha-helix structure
| [[CV:PBETA|PBETA]]
| content of the parallel beta-sheet structure
|-
| [[CV:ABETA|ABETA]]
| content of the antiparallel beta-sheet structure
|
| -->
|-
|-
| colspan="4" style="text-align: center; background-color: #CCCCFF;" | '''[[Ring Puckering]]'''
| colspan="4" style="text-align: center; background-color: #CCCCFF;" | '''[[Ring Puckering]]'''
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|-
|-
| [[CV:PUCK6P|PUCK6P]]
| [[CV:PUCK6P|PUCK6P]]
| puckering azimuthal angle of six-membered ring
| puckering azimuthal angle of the six-membered ring
| [[CV:PUCK5P|PUCK5P]]
| [[CV:PUCK5P|PUCK5P]]
| puckering azimuthal angle of five-membered ring
| puckering azimuthal angle of the five-membered ring
|-
|-
| [[CV:PUCK6T|PUCK6T]]
| [[CV:PUCK6T|PUCK6T]]
| puckering polar angle of six-membered ring
| puckering polar angle of the six-membered ring
|
|
|
|
|-
| colspan="4" style="text-align: center; background-color: #CCCCFF;" | '''Special'''
|-
| style="width: 5em;" | '''Type'''
| '''Description'''
| style="width: 5em;" | '''Type'''
| '''Description'''
|-
| [[CV:WORMPOS|WORMPOS]]
| parametrical position of an axle inside a macrocycle
| [[CV:WORMANG|WORMANG]]
| orientation of an axle inside a macrocycle
|-
|-
|-
| colspan="4" style="text-align: center; background-color: #CCCCFF;" | '''Energy'''
| colspan="4" style="text-align: center; background-color: #CCCCFF;" | '''Energy'''
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| [[CV:DIV|DIV]]
| [[CV:DIV|DIV]]
| ratio of two collective variables
| ratio of two collective variables
|-
| [[CV:FSWITCH|FSWITCH]]
| Fermi-like switch function
| [[CV:RSWITCH|RSWITCH]]
| rational switch function
|}
|}
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