HYDRONIUM_SHELL

Section to define the formation of a hydronium as a collective variable. Number of oxygens in the 1st shell of the hydronium. Adapted from Equation (3) in Supplementary Info of J. Am. Chem. Soc.,128, 2006, 11318, i.e. omitting the cutoff function and summing only over the oxygens of water. [Edit on GitHub]

Keywords

HYDROGENS
LAMBDA
NH
OXYGENS
PM
POH
POO
QM
QOH
QOO
ROH
ROO

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.

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LAMBDA

Type: real
Default: 1.00000000E+001
Usage: LAMBDA {real}

Description: Specify the LAMBDA parameter in the hydronium function.

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NH

Type: real
Default: 3.00000000E+000
Usage: NH {real}

Description: Specifies the NH parameter in the M function.

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OXYGENS

Type: integer[ ]
Repeatable: yes
Usage: OXYGENS {integer} {integer} ..

Description: Specifies indexes of atoms building the coordination variable. Oxygens of the water molecules.

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PM

Type: integer
Default: 8
Aliases: EXPON_NUMERATOR
Usage: pM {integer}

Description: Sets the value of the numerator of the exponential factor in the M function.

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POH

Type: integer
Default: 6
Aliases: EXPON_NUMERATORB
Usage: pOH {integer}

Description: Sets the value of the numerator of the exponential factor in the coordination function: number of hydrogens per water molecule.

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POO

Type: integer
Default: 6
Aliases: EXPON_NUMERATORA
Usage: pOO {integer}

Description: Sets the value of the numerator of the exponential factor in the coordination function: number of oxygens per water oxygen.

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QM

Type: integer
Default: 16
Aliases: EXPON_DENOMINATOR
Usage: qM {integer}

Description: Sets the value of the denominator of the exponential factor in the M function.

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QOH

Type: integer
Default: 12
Aliases: EXPON_DENOMINATORB
Usage: qOH {integer}

Description: Sets the value of the denominator of the exponential factor in the coordination function: number of hydrogens per water molecule.

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QOO

Type: integer
Default: 12
Aliases: EXPON_DENOMINATORA
Usage: qOO {integer}

Description: Sets the value of the denominator of the exponential factor in the coordination function: number of oxygens per water oxygen.

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ROH

Type: real
Default: 3.00000000E+000 [bohr]
Usage: ROH {real}

Description: Specifies the rc parameter in the coordination function: number of hydrogens per water molecule.

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ROO

Type: real
Default: 3.00000000E+000 [bohr]
Usage: ROO {real}

Description: Specifies the rc parameter in the coordination function: number of oxygens per water oxygen.

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