Collective Variables: Difference between revisions
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Collective variables (CVs) define a subset of configuration space in which 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 | 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 the section defines a type of CV. The section contains the name key containing a unique CV name and other keys specific | 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: | Extra documentation: | ||
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| 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:ORAD|ORAD]] | | [[CV:ORAD|ORAD]] | ||
| radial distance in oriented coordinate system | | radial distance in the oriented coordinate system | ||
| [[CV:POS|POS]] | | [[CV:POS|POS]] | ||
| absolute position | | absolute position | ||
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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 | | projection into essential vector | ||
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|- | |- | ||
| [[CV:ALPHA|ALPHA]] | | [[CV:ALPHA|ALPHA]] | ||
| content of alpha-helix structure | | content of the alpha-helix structure | ||
| [[CV:PBETA|PBETA]] | | [[CV:PBETA|PBETA]] | ||
| content of parallel beta-sheet structure | | content of the parallel beta-sheet structure | ||
|- | |- | ||
| [[CV:ABETA|ABETA]] | | [[CV:ABETA|ABETA]] | ||
| content of antiparallel beta-sheet structure | | content of the antiparallel beta-sheet structure | ||
| | | | ||
| --> | | --> | ||
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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 | ||
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