Collective Variables: Difference between revisions

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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===
Line 30: Line 35:
| [[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'''
Line 52: Line 62:
| [[CV:ANG|ANG]]
| [[CV:ANG|ANG]]
| angle among three points
| angle among three points
| [[CV:ANG2|ANG2]]
| angle between two vectors defined by four points
|-
| [[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]]
| angle between two planes
| angle between two planes
|-
| [[CV:PVANG|PVANG]]
| [[CV:PVANG|PVANG]]
| angle between plane and vector
| angle between plane and vector
|
|
|-
|-
| colspan="4" style="text-align: center; background-color: #CCCCFF;" | '''Coordination Numbers'''
| colspan="4" style="text-align: center; background-color: #CCCCFF;" | '''Coordination Numbers'''
Line 113: Line 128:
| 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'''
Line 127: Line 142:
| '''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]]'''
Line 146: Line 197:
|-
|-
| [[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'''
Line 183: Line 247:
| [[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
|}
|}

Latest revision as of 14:48, 21 July 2021

Navigation: Documentation / Collective Variables

Distance

Angle

Coordination

Shape

Nucleic Acids

Puckering

Special

Energy

Algebra

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:

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 OPOS2 absolute position in the superimposed coordinate system
ORAD radial distance in the oriented coordinate system ORAD2 radial distance in the superimposed 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
Special
Type Description Type Description
WORMPOS parametrical 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 switch function RSWITCH rational switch function
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