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

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

Keyword descriptions

HYDROGENS: integer

Keyword can be repeated.

Usage: HYDROGENS {integer} {integer} ..

Specifies indexes of atoms building the coordination variable. Hydrogens of the water molecules and of the carboxyl groups. [Edit on GitHub]

LAMBDA: real = 1.00000000E+001 

Aliases: LAMBDA

Usage: LAMBDA {real}

Specifies the LAMBDA parameter carboxylic acid function. [Edit on GitHub]

NC: real = 9.00000000E-001 

Usage: NC {real}

Specifies the NC parameter in the cutoff function. [Edit on GitHub]

NH: real = 2.20000000E+000 

Usage: NH {real}

Specifies the NH parameter in the M function. [Edit on GitHub]

OXYGENS_ACID: integer

Keyword can be repeated.

Usage: OXYGENS {integer} {integer} ..

Specifies indexes of atoms building the coordination variable. Oxygens of the carboxyl groups. [Edit on GitHub]

OXYGENS_WATER: integer

Keyword can be repeated.

Usage: OXYGENS {integer} {integer} ..

Specifies indexes of atoms building the coordination variable. Oxygens of the water molecules. [Edit on GitHub]

PAOH: integer = 6 

Usage: pAOH {integer}

Sets the value of the numerator of the exponential factor in the coordination function: number of hydrogens per carboxyl group. [Edit on GitHub]

PCUT: integer = 6 

Usage: pCUT {integer}

Sets the value of the numerator of the exponential factor in the cutoff function. [Edit on GitHub]

PM: integer = 8 

Usage: pM {integer}

Sets the value of the numerator of the exponential factor in the M function. [Edit on GitHub]

POO: integer = 6 

Usage: pOO {integer}

Sets the value of the numerator of the exponential factor in the coordination function: number of oxygens per water oxygen. [Edit on GitHub]

PWOH: integer = 8 

Usage: pWOH {integer}

Sets the value of the numerator of the exponential factor in the coordination function: number of hydrogens per water molecule. [Edit on GitHub]

QAOH: integer = 14 

Usage: qAOH {integer}

Sets the value of the denominator of the exponential factor in the coordination function: number of hydrogens per carboxyl group. [Edit on GitHub]

QCUT: integer = 12 

Usage: qCUT {integer}

Sets the value of the denominator of the exponential factor in the cutoff function. [Edit on GitHub]

QM: integer = 16 

Usage: qM {integer}

Sets the value of the denominator of the exponential factor in the M function. [Edit on GitHub]

QOO: integer = 12 

Usage: qOO {integer}

Sets the value of the denominator of the exponential factor in the coordination function: number of oxygens per water oxygen. [Edit on GitHub]

QWOH: integer = 16 

Usage: qWOH {integer}

Sets the value of the denominator of the exponential factor in the coordination function: number of hydrogens per water molecule. [Edit on GitHub]

RAOH: real = 2.40000000E+000 [bohr]

Usage: RAOH {real}

Specifies the rc parameter in the coordination function: number of hydrogens per carboxyl group. [Edit on GitHub]

ROO: real = 5.50000000E+000 [bohr]

Usage: ROO {real}

Specifies the rc parameter in the coordination function: number of oxygens per water oxygen. [Edit on GitHub]

RWOH: real = 2.40000000E+000 [bohr]

Usage: RWOH {real}

Specifies the rc parameter in the coordination function: number of hydrogens per water molecule. [Edit on GitHub]