Section REACTION_PATH

• 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.

• Section path: CP2K_INPUT / FORCE_EVAL / SUBSYS / COLVAR / REACTION_PATH

• This section cannot be repeated and cannot be optional.

• This section cites the following reference: [Branduardi2007]

• Subsections

  • COLVAR
  • FRAME
  • MAP

• Keywords

  • ALIGN_FRAMES
  • ATOMS
  • DISTANCES_RMSD
  • FUNCTION
  • LAMBDA
  • RANGE
  • RMSD
  • STEP_SIZE
  • SUBSET_TYPE
  • VARIABLE

• Keyword descriptions

  ALIGN_FRAMES
  	ALIGN_FRAME
  	Whether the reference frames should be aligned to minimize the RMSD
  	This optional keyword cannot be repeated and it expects precisely one logical.
  	The lone keyword behaves as a switch to .TRUE.
  	Default value: .FALSE.

  ATOMS
  	ATOMS {INTEGER} {INTEGER} ..
  	Specify indexes of atoms building the subset.
  	This optional keyword can be repeated and it expects a list of integers.

  DISTANCES_RMSD
  	DISTANCES_RMSD T
  	This optional keyword cannot be repeated and it expects precisely one logical.
  	The lone keyword behaves as a switch to .TRUE.
  	Default value: .FALSE.

  FUNCTION
  	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.
  	This optional keyword can be repeated and it expects precisely one string.
  	Default value: 0

  LAMBDA
  	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.
  	This required keyword cannot be repeated and it expects precisely one real.
  	Default value: 5.00000000E+00

  RANGE
  	RANGE <REAL> <REAL>
  	The range of VARIABLE used for the parametrisation.
  	This optional keyword cannot be repeated and it expects precisely 2 reals.

  RMSD
  	RMSD T
  	This optional keyword cannot be repeated and it expects precisely one logical.
  	The lone keyword behaves as a switch to .TRUE.
  	Default value: .FALSE.

  STEP_SIZE
  	STEP_SIZE {REAL}
  	Step size in the numerical integration, a few thousand points are common, and the proper number also depends on LAMBDA.
  	This required keyword cannot be repeated and it expects precisely one real.
  	Default value: 1.00000000E-02

  SUBSET_TYPE
  	SUBSET_TYPE ALL
  	Define the subsytem used to compute the RMSD
  	This optional keyword cannot be repeated and it expects precisely one keyword.
  	Default value: ALL
  	List of valid keywords: ALL LIST

  VARIABLE
  	VARIABLE T
  	Specifies the name of the variable that parametrises the FUNCTION defining the reaction path.
  	This optional keyword cannot be repeated and it expects precisely one word.