DISTANCE_FROM_PATH

References: Branduardi2007

Section defining the distance from a one dimensional reaction path in an Q-dimensional space of colvars. Constraining this colvar, allows to sample the space equidistant 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

Type: logical
Default: F
Lone keyword: T
Usage: ALIGN_FRAMES

Description: Whether the reference frames should be aligned to minimize the RMSD

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ATOMS

Type: integer[ ]
Repeatable: yes
Usage: ATOMS {integer} {integer} ..

Description: Specify indexes of atoms building the subset.

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DISTANCES_RMSD

Type: logical
Default: F
Lone keyword: T
Usage: DISTANCES_RMSD T

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FUNCTION

Type: string
Default: 0
Repeatable: yes
Usage: FUNCTION (sin(T+2)+2*T)

Description: 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.

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LAMBDA

Type: real
Default: 5.00000000E+000
Usage: LAMBDA {real}

Description: 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.

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RANGE

Type: real[2]
Usage: RANGE

Description: The range of VARIABLE used for the parametrisation.

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RMSD

Type: logical
Default: F
Lone keyword: T
Usage: RMSD T

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STEP_SIZE

Type: real
Default: 1.00000000E-002
Usage: STEP_SIZE {real}

Description: Step size in the numerical integration, a few thousand points are common, and the proper number also depends on LAMBDA.

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SUBSET_TYPE

Type: enum
Default: ALL
Usage: SUBSET_TYPE ALL

Description: Define the subsytem used to compute the RMSD

Valid values:

• ALL

• LIST

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VARIABLE

Type: string
Usage: VARIABLE T

Description: Specifies the name of the variable that parametrises the FUNCTION defining the reaction path.

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