Section ACID_HYDRONIUM_SHELL

• Section to define the dissociation of a carboxylic acid in water. Number of oxygens in the 1st shell of the hydronium. Equation (3) in Supplementary Info of J. Am. Chem. Soc.,128, 2006, 11318. Similar to the HYDRONIUM colvar, but with modification for the acid.

• Section path: CP2K_INPUT / FORCE_EVAL / SUBSYS / COLVAR / COMBINE_COLVAR / COLVAR / ACID_HYDRONIUM_SHELL

• This section cannot be repeated.

• Subsections

  • none

• Keywords

  • HYDROGENS
  • LAMBDA
  • NC
  • NH
  • OXYGENS_ACID
  • OXYGENS_WATER
  • PAOH
  • PCUT
  • PM
  • POO
  • PWOH
  • QAOH
  • QCUT
  • QM
  • QOO
  • QWOH
  • RAOH
  • ROO
  • RWOH

• Keyword descriptions

  HYDROGENS
  	HYDROGENS {Integer} ...
  	Specifies indexes of atoms building the coordination variable. Hydrogens of the water molecules and of the carboxyl groups.
  	This keyword can be repeated and it expects a list of integers.

  LAMBDA
  	LAMBDA {Real}
  	Specifies the LAMBDA parameter carboxylic acid function.
  	This keyword cannot be repeated and it expects precisely one real.
  	Default value: 1.00000000E+001
  	Alias names for this keyword: LAMBDA

  NC
  	NC {Real}
  	Specifies the NC parameter in the cutoff function.
  	This keyword cannot be repeated and it expects precisely one real.
  	Default value: 9.00000000E-001

  NH
  	NH {Real}
  	Specifies the NH parameter in the M function.
  	This keyword cannot be repeated and it expects precisely one real.
  	Default value: 2.20000000E+000

  OXYGENS_ACID
  	OXYGENS_ACID {Integer} ...
  	Specifies indexes of atoms building the coordination variable. Oxygens of the carboxyl groups.
  	This keyword can be repeated and it expects a list of integers.

  OXYGENS_WATER
  	OXYGENS_WATER {Integer} ...
  	Specifies indexes of atoms building the coordination variable. Oxygens of the water molecules.
  	This keyword can be repeated and it expects a list of integers.

  PAOH
  	PAOH {Integer}
  	Sets the value of the numerator of the exponential factor in the coordination function: number of hydrogens per carboxyl group.
  	This keyword cannot be repeated and it expects precisely one integer.
  	Default value: 6

  PCUT
  	PCUT {Integer}
  	Sets the value of the numerator of the exponential factorin the cutoff function.
  	This keyword cannot be repeated and it expects precisely one integer.
  	Default value: 6

  PM
  	PM {Integer}
  	Sets the value of the numerator of the exponential factor in the M function.
  	This keyword cannot be repeated and it expects precisely one integer.
  	Default value: 8

  POO
  	POO {Integer}
  	Sets the value of the numerator of the exponential factor in the coordination function: number of oxygens per water oxygen.
  	This keyword cannot be repeated and it expects precisely one integer.
  	Default value: 6

  PWOH
  	PWOH {Integer}
  	Sets the value of the numerator of the exponential factor in the coordination function: number of hydrogens per water molecule.
  	This keyword cannot be repeated and it expects precisely one integer.
  	Default value: 8

  QAOH
  	QAOH {Integer}
  	Sets the value of the denominator of the exponential factor in the coordination function: number of hydrogens per carboxyl group.
  	This keyword cannot be repeated and it expects precisely one integer.
  	Default value: 14

  QCUT
  	QCUT {Integer}
  	Sets the value of the denominator of the exponential factorin the cutoff function.
  	This keyword cannot be repeated and it expects precisely one integer.
  	Default value: 12

  QM
  	QM {Integer}
  	Sets the value of the denominator of the exponential factor in the M function.
  	This keyword cannot be repeated and it expects precisely one integer.
  	Default value: 16

  QOO
  	QOO {Integer}
  	Sets the value of the denominator of the exponential factor in the coordination function: number of oxygens per water oxygen.
  	This keyword cannot be repeated and it expects precisely one integer.
  	Default value: 12

  QWOH
  	QWOH {Integer}
  	Sets the value of the denominator of the exponential factor in the coordination function: number of hydrogens per water molecule.
  	This keyword cannot be repeated and it expects precisely one integer.
  	Default value: 16

  RAOH
  	RAOH {Real}
  	Specifies the rc parameter in the coordination function: number of hydrogens per carboxyl group.
  	This keyword cannot be repeated and it expects precisely one real.
  	Default value: 2.40000000E+000
  	Default unit: [bohr]

  ROO
  	ROO {Real}
  	Specifies the rc parameter in the coordination function: number of oxygens per water oxygen.
  	This keyword cannot be repeated and it expects precisely one real.
  	Default value: 5.50000000E+000
  	Default unit: [bohr]

  RWOH
  	RWOH {Real}
  	Specifies the rc parameter in the coordination function: number of hydrogens per water molecule.
  	This keyword cannot be repeated and it expects precisely one real.
  	Default value: 2.40000000E+000
  	Default unit: [bohr]