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.
The default is to use the colvars defined in the COLVAR subsections, which requires FUNCTION, VARIABLE, RANGE, STEP_SIZE keywords and optionally the MAP print key. Switching on either RMSD or DISTANCES_RMSD (which are mutually exclusive) instead requires the SUBSET_TYPE, ALIGN_FRAMES (and optionally ATOMS) keywords and the FRAME subsections. The LAMBDA keyword is always required for each of the three possibilities. [Edit on GitHub]
Keywords
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 [Edit on GitHub]
ATOMS
Type: integer[ ]
Repeatable: yes
Usage: ATOMS {integer} {integer} ..
Description: Specify indexes of atoms building the subset. [Edit on GitHub]
DISTANCES_RMSD
Type: logical
Default: F
Lone keyword: T
Usage: DISTANCES_RMSD T
Description: Whether to use distances RMSD instead of COLVARs. [Edit on GitHub]
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 defined in the COLVAR subsections. The VARIABLE (e.g. T) which parametrises the curve can be used as the target of a constraint. Mathematical Operators recognized are +, -, *, /, ^ or alternatively **, whereas symbols for brackets must be (). The function parser recognizes the Fortran 90 intrinsic functions abs, min, max, exp, log10, log, sqrt, sinh, cosh, tanh, sin, cos, tan, asin, acos, atan2, atan, erf, erfc. Parsing for intrinsic functions is not case sensitive.
[Edit on GitHub]
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. [Edit on GitHub]
RANGE
Type: real[2]
Usage: RANGE <REAL> <REAL>
Description: The range of VARIABLE used for the parametrisation. [Edit on GitHub]
RMSD
Type: logical
Default: F
Lone keyword: T
Usage: RMSD T
Description: Whether to use RMSD instead of COLVARs. [Edit on GitHub]
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. [Edit on GitHub]
SUBSET_TYPE
Type: enum
Default: ALL
Usage: SUBSET_TYPE ALL
Description: Define the subsytem used to compute the RMSD [Edit on GitHub]
Valid values:
ALLLIST
VARIABLE
Type: string
Usage: VARIABLE T
Description: Specifies the name of the variable that parametrises the FUNCTION defining the reaction path. All Q functions must use this variable. [Edit on GitHub]