Paths
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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.
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 [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 later 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.
[PATH]
| Key | Default value | Type | Description |
| name | string | unique PATH name | |
| ncvs | integer | Number of CVs used to describe point along the path. At least two collective variables must be used. | |
| nbeads | integer | Number of points along path. This number determines the level of path discretization. | |
| names | string list | List of names of collective variables used to construct point along the path. | |
| types | string list | List of types of collective variables. | |
| min | real list | Minimum allowed values of collective variables. The number of entries must be the same as the number of collective variables. | |
| max | real list | Maximum allowed values of collective variables. | |
| maxmove | 0.0 | real list | Maximum allowed changes of collective variable values. This option is disabled if the value is zero or has negative value. |
| flexible* | real list | List of values of collective variables defining flexible point along the path. | |
| permanent* | real list | List of values of collective variables defining permanent point along the path. In current implementation, the permanent points can be only at the path ends. |
Keys in bold are mandatory. *) At least two points must be provided.
Examples
! this is an incomplete path [PATH] name p1 nbeads 8 ncvs 2 names d1 d2 types DIS DIS min 3.0 3.0 max 11.5 11.5 maxmov 0.1 0.1 permanent 3.0 11.5 flexible 10.0 5.0 permanent 11.5 3.0 ! this is a complete path [PATH] name p1 ncvs 2 nbeads 8 names d1 d2 types DIS DIS min 0.3000000E+01 0.3000000E+01 max 0.1150000E+02 0.1150000E+02 maxmove 0.1000000E+00 0.1000000E+00 permanent 0.3000000E+01 0.1150000E+02 flexible 0.4407419E+01 0.1046566E+02 flexible 0.5750460E+01 0.9371341E+01 flexible 0.7029123E+01 0.8217038E+01 flexible 0.8243409E+01 0.7002752E+01 flexible 0.9393317E+01 0.5728484E+01 flexible 0.1047885E+02 0.4394233E+01 permanent 0.1150000E+02 0.3000000E+01