Paths: Difference between revisions
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Paths define subset of configuration space in which the free energy is being calculated or collective variables are manipulated. It depends on used method if paths are static or flexible during calculations. | Paths define a subset of configuration space in which the free energy is being calculated or collective variables are manipulated. It depends on the used method if paths are static or flexible during calculations. | ||
The path definition can be read either from the input file or from an external file. The mode used will depend on the setup provided in the [[General setup|[files]]] section. If the fpathsdef key contains the name of the group (e.g. string starting with the "{" character) then the path setup will be read from this group provided in the input file. Otherwise the path setup is read from a file with the name provided by the fpathsdef key. In the | The path definition can be read either from the input file or from an external file. The mode used will depend on the setup provided in the [[General setup|[files]]] section. If the fpathsdef key contains the name of the group (e.g. string starting with the "{" character) then the path setup will be read from this group provided in the input file. Otherwise, the path setup is read from a file with the name provided by the fpathsdef key. In the latter case, the path definition must be in the {MAIN} group (which is implicit and can be omitted in the file). | ||
The group or file can contain several paths. Each path is specified in a single section. The name of this section is PATH. The path might be provided in a complete or an incomplete forms. In the complete form, the number of explicitly specified points (via permanent or flexible keys) is exactly equal to the value of the nbeads key. In all other cases, the path is incomplete. Incomplete paths are reconstructed prior further usage. Cubic splines are used to generate smooth continuous path along which beads are put into equidistant positions. | The group or file can contain several paths. Each path is specified in a single section. The name of this section is PATH. The path might be provided in a complete or an incomplete forms. In the complete form, the number of explicitly specified points (via permanent or flexible keys) is exactly equal to the value of the nbeads key. In all other cases, the path is incomplete. Incomplete paths are reconstructed prior further usage. Cubic splines are used to generate smooth continuous path along which beads are put into equidistant positions. | ||