REACTION_PATH

References: Branduardi2007

Section defining a one dimensional reaction path in an Q-dimensional space of colvars. Constraining this colvar, allows to sample the space orthogonal to the reaction path, both in the Q-dimensional colvar and 3N-Q remaining coordinates. For the details of the function see cited literature. [Edit on GitHub]

Subsections

• COLVAR
• FRAME
• MAP

Keywords

• ALIGN_FRAMES

• ATOMS

• DISTANCES_RMSD

• FUNCTION

• LAMBDA

• RANGE

• RMSD

• STEP_SIZE

• SUBSET_TYPE

• VARIABLE

Keyword descriptions

ALIGN_FRAMES: logical = F

Lone keyword: T

Usage: ALIGN_FRAME

Whether the reference frames should be aligned to minimize the RMSD [Edit on GitHub]

ATOMS: integer

Keyword can be repeated.

Usage: ATOMS {integer} {integer} ..

Specify indexes of atoms building the subset. [Edit on GitHub]

DISTANCES_RMSD: logical = F

Lone keyword: T

Usage: DISTANCES_RMSD T

[Edit on GitHub]

FUNCTION: string = 0

Keyword can be repeated.

Usage: FUNCTION (sin(T+2)+2*T)

Specifies the ith element of the vector valued function that defines the reaction path. This keyword needs to repeat exactly Q times, and the order must match the order of the colvars. The VARIABLE (e.g. T) which parametrises the curve can be used as the target of a constraint. [Edit on GitHub]

LAMBDA: real = 5.00000000E+000

Usage: LAMBDA {real}

Specifies the exponent of the Gaussian used in the integral representation of the colvar. The shape of the space orthogonal to the reaction path is defined by this choice. In the limit of large values, it is given by the plane orthogonal to the path. In practice, modest values are required for stable numerical integration. [Edit on GitHub]

RANGE: real[2]

Usage: RANGE

The range of VARIABLE used for the parametrisation. [Edit on GitHub]

RMSD: logical = F

Lone keyword: T

Usage: RMSD T

[Edit on GitHub]

STEP_SIZE: real = 1.00000000E-002

Usage: STEP_SIZE {real}

Step size in the numerical integration, a few thousand points are common, and the proper number also depends on LAMBDA. [Edit on GitHub]

SUBSET_TYPE: enum = ALL

Usage: SUBSET_TYPE ALL

Valid values:

• ALL

• LIST

Define the subsytem used to compute the RMSD [Edit on GitHub]

VARIABLE: string

Usage: VARIABLE T

Specifies the name of the variable that parametrises the FUNCTION defining the reaction path. [Edit on GitHub]