Collective Variables: Difference between revisions
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{{CVS}}__NOEDITSECTION__ | {{CVS}}__NOEDITSECTION__ | ||
Collective variables (CVs) define subset of configuration space in which | 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 later 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 for a given CV type. | ||
Special documentation: | |||
* [[Nucleic Acids]] | |||
* [[Ring Puckering]] | |||
===Supported Types=== | ===Supported Types=== | ||
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| simple base pair parameters | | simple base pair parameters | ||
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| colspan="4" style="text-align: center; background-color: #CCCCFF;" | '''[[Ring Puckering]]''' | | colspan="4" style="text-align: center; background-color: #CCCCFF;" | '''[[Ring Puckering]]''' | ||