Paths

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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 [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.

[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