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. [Edit on GitHub]
Keywords
Keyword descriptions
- HYDROGENS
Type: integer[ ]
Repeatable: yes
Usage: HYDROGENS {integer} {integer} ..Description: Specifies indexes of atoms building the coordination variable. Hydrogens of the water molecules and of the carboxyl groups.
- LAMBDA
Type: real
Default: 1.00000000E+001
Aliases: LAMBDA
Usage: LAMBDA {real}Description: Specifies the LAMBDA parameter carboxylic acid function.
- NC
Type: real
Default: 9.00000000E-001
Usage: NC {real}Description: Specifies the NC parameter in the cutoff function.
- NH
Type: real
Default: 2.20000000E+000
Usage: NH {real}Description: Specifies the NH parameter in the M function.
- OXYGENS_ACID
Type: integer[ ]
Repeatable: yes
Usage: OXYGENS_ACID {integer} {integer} ..Description: Specifies indexes of atoms building the coordination variable. Oxygens of the carboxyl groups.
- OXYGENS_WATER
Type: integer[ ]
Repeatable: yes
Usage: OXYGENS_WATER {integer} {integer} ..Description: Specifies indexes of atoms building the coordination variable. Oxygens of the water molecules.
- PAOH
Type: integer
Default: 6
Usage: pAOH {integer}Description: Sets the value of the numerator of the exponential factor in the coordination function: number of hydrogens per carboxyl group.
- PCUT
Type: integer
Default: 6
Usage: pCUT {integer}Description: Sets the value of the numerator of the exponential factor in the cutoff function.
- PM
Type: integer
Default: 8
Usage: pM {integer}Description: Sets the value of the numerator of the exponential factor in the M function.
- POO
Type: integer
Default: 6
Usage: pOO {integer}Description: Sets the value of the numerator of the exponential factor in the coordination function: number of oxygens per water oxygen.
- PWOH
Type: integer
Default: 8
Usage: pWOH {integer}Description: Sets the value of the numerator of the exponential factor in the coordination function: number of hydrogens per water molecule.
- QAOH
Type: integer
Default: 14
Usage: qAOH {integer}Description: Sets the value of the denominator of the exponential factor in the coordination function: number of hydrogens per carboxyl group.
- QCUT
Type: integer
Default: 12
Usage: qCUT {integer}Description: Sets the value of the denominator of the exponential factor in the cutoff function.
- QM
Type: integer
Default: 16
Usage: qM {integer}Description: Sets the value of the denominator of the exponential factor in the M function.
- QOO
Type: integer
Default: 12
Usage: qOO {integer}Description: Sets the value of the denominator of the exponential factor in the coordination function: number of oxygens per water oxygen.
- QWOH
Type: integer
Default: 16
Usage: qWOH {integer}Description: Sets the value of the denominator of the exponential factor in the coordination function: number of hydrogens per water molecule.
- RAOH
Type: real
Default: 2.40000000E+000 [bohr]
Usage: RAOH {real}Description: Specifies the rc parameter in the coordination function: number of hydrogens per carboxyl group.
- ROO
Type: real
Default: 5.50000000E+000 [bohr]
Usage: ROO {real}Description: Specifies the rc parameter in the coordination function: number of oxygens per water oxygen.
- RWOH
Type: real
Default: 2.40000000E+000 [bohr]
Usage: RWOH {real}Description: Specifies the rc parameter in the coordination function: number of hydrogens per water molecule.