GHBFIX

This is part of the colvar module

Calculate the GHBFIX interaction energy among GROUPA and GROUPB using a potential defined in Kührová et al., Improving the performance of the AMBER RNA force field by tuning the hydrogen-bonding interactions, JCTC, 2019. Essentially it is a switching function being -1 for small distances and 0 for large distances with a smooth interpolation in the middle. This can be scaled as desired by specifying interaction scaling parameters and energy units.

This collective variable can be used to analyze hydrogen bond interactions, or to generate bias potentials. Notice that the value of the GHBFIX is returned in plumed units (see UNITS), if not specified differently via ENERGY_UNITS.

Examples

This example prints the GHBFIX interaction in kcal/mol between two groups of atoms using D_0, D_MAX and C It is applied in the functional form introduced in the pioneering paper. The types of atoms 1-6 should be defined in typesTable_examples.dat while their interaction parameters should be defined in scalingParameters_examples.dat in kBT units.

Click on the labels of the actions for more information on what each action computes

#SETTINGS AUXFOLDER=regtest/basic/rt-ghbfix
gh: GHBFIX 
PAIR
( default=off ) Pair only 1st element of the 1st group with 1st element in the second,
etc 
 
GROUPA
First list of atoms. 
=1,2,3 
GROUP
 could not find this keyword 
=4,5,6 
D_0
 could not find this keyword 
=0.2 
D_MAX
compulsory keyword 
the value of D_MAX in the switching function 
=0.3 
C
compulsory keyword 
the value of C in the switching function 
=0.8 
TYPES
compulsory keyword 
the value of TYPES in the switching function 
=typesTable_examples.dat 
PARAMS
compulsory keyword 
the value of PARAMS in the switching function 
=scalingParameters_examples.dat 
ENERGY_UNITS
the value of ENERGY_UNITS in the switching function 
=kcal/mol  You cannot view the components that are calculated by each action for this input file. Sorry 
PRINT 
FILE
the name of the file on which to output these quantities 
=output 
ARG
compulsory keyword 
the labels of the values that you would like to print to the file 
=gh  You cannot view the components that are calculated by each action for this input file. Sorry 

Glossary of keywords and components

Description of components

By default the value of the calculated quantity can be referenced elsewhere in the input file by using the label of the action. Alternatively this Action can be used to calculate the following quantities by employing the keywords listed below. These quantities can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the quantity required from the list below.

Quantity	Description
.#!value	the GHBFIX interaction energy between the atoms in GROUPA and GROUPB

The atoms involved can be specified using

GROUPA	First list of atoms. For more information on how to specify lists of atoms see Groups and Virtual Atoms
GROUPB	Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted). For more information on how to specify lists of atoms see Groups and Virtual Atoms

Compulsory keywords

TYPES	the value of TYPES in the switching function
PARAMS	the value of PARAMS in the switching function
D_MAX	the value of D_MAX in the switching function
D_0	the value of D_0 in the switching function
C	the value of C in the switching function

Options

NUMERICAL_DERIVATIVES	( default=off ) calculate the derivatives for these quantities numerically
NOPBC	( default=off ) ignore the periodic boundary conditions when calculating distances
SERIAL	( default=off ) Perform the calculation in serial - for debug purpose
PAIR	( default=off ) Pair only 1st element of the 1st group with 1st element in the second, etc
NLIST	( default=off ) Use a neighbor list to speed up the calculation
NL_CUTOFF	The cutoff for the neighbor list
NL_STRIDE	The frequency with which we are updating the atoms in the neighbor list
ENERGY_UNITS	the value of ENERGY_UNITS in the switching function