Action: GHBFIX

Module colvar
Description Usage
Calculate the GHBFIX interaction energy between GROUPA and GROUPB used in 0 tutorialsused in 3 eggs
output value type
the GHBFIX interaction energy between the atoms in GROUPA and GROUPB scalar

Input

The atoms that serve as the input for this action are specified using one or more of the keywords in the following table.

Keyword Type Description
GROUPA atoms First list of atoms
GROUPB atoms Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)

Further details and examples

Calculate the GHBFIX interaction energy between GROUPA and GROUPB

The GHBFIX interaction energy between GROUPA and GROUPB is computed using a potential that is defiend in the paper cited in the bibliogrpahy below. The potential introduced in that paper is essentially a switching function that is -1 for small distances and 0 for large distances with a smooth interpolation in the middle. This function 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), unless the ENERGY_UNITS keyword is employed.

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
tested on2.11
#SETTINGS INPUTFILES=regtest/basic/rt-ghbfix/typesTable_examples.dat,regtest/basic/rt-ghbfix/scalingParameters_examples.dat
gh: GHBFIXCalculate the GHBFIX interaction energy between GROUPA and GROUPB More details ...
   PAIR Pair only 1st element of the 1st group with 1st element in the second, etc GROUPAFirst list of atoms=1,2,3 GROUP=4,5,6 D_0the value of D_0 in the switching function=0.2 D_MAXthe value of D_MAX in the switching function=0.3 Cthe value of C in the switching function=0.8
   TYPESthe value of TYPES in the switching function=
regtest/basic/rt-ghbfix/typesTable_examples.dat
 Click here to see an extract from this file.
  
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FILE: regtest/basic/rt-ghbfix/typesTable_examples.dat
    
#! FIELDS itype
 type0
 type0
 type1
 type1
 type2
 type2

  

   PARAMSthe value of PARAMS in the switching function=
regtest/basic/rt-ghbfix/scalingParameters_examples.dat
 Click here to see an extract from this file.
  
  ×  
FILE: regtest/basic/rt-ghbfix/scalingParameters_examples.dat
    
#! FIELDS itype jtype eta
 type0 type1 0.5
 type0 type2 -1.0
 type1 type2 1.5

  

   ENERGY_UNITSthe value of ENERGY_UNITS in the switching function=kcal/mol
...
PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=output ARGthe labels of the values that you would like to print to the file=gh

References

More information about how this action can be used is available in the following articles: - P. Kührová, V. Mlýnský, M. Zgarbová, M. Krepl, G. Bussi, R. B. Best, M. Otyepka, J. Šponer, P. Banáš, Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions. Journal of Chemical Theory and Computation. 15, 3288–3305 (2019)

Syntax

The following table describes the keywords and options that can be used with this action

Keyword Type Default Description
GROUPA input none First list of atoms
GROUPB input none Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
TYPES compulsory none the value of TYPES in the switching function
PARAMS compulsory none the value of PARAMS in the switching function
D_MAX compulsory none the value of D_MAX in the switching function
D_0 compulsory none the value of D_0 in the switching function
C compulsory none the value of C in the switching function
NUMERICAL_DERIVATIVES optional false calculate the derivatives for these quantities numerically
NOPBC optional false ignore the periodic boundary conditions when calculating distances
SERIAL optional false Perform the calculation in serial - for debug purpose
PAIR optional false Pair only 1st element of the 1st group with 1st element in the second, etc
NLIST optional false Use a neighbor list to speed up the calculation
NL_CUTOFF optional not used The cutoff for the neighbor list
NL_STRIDE optional not used The frequency with which we are updating the atoms in the neighbor list
ENERGY_UNITS optional not used the value of ENERGY_UNITS in the switching function