Action: HBPAMM_SH

Module pamm
Description Usage
Calculate the number of hydrogen bonds each hydrogen participates in using the HBPamm method used in 0 tutorialsused in 0 eggs
output value type
a vector specifiying the number of hydrogen bonds each of the specified atoms participates within vector

Output components

This action can calculate the values in the following table when the associated keyword is included in the input for the action. These values can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the value required from the list below.

Name Type Keyword Description
lessthan scalar LESS_THAN the number of colvars that have a value less than a threshold
morethan scalar MORE_THAN the number of colvars that have a value more than a threshold
altmin scalar ALT_MIN the minimum value of the cv
min scalar MIN the minimum colvar
max scalar MAX the maximum colvar
between scalar BETWEEN the number of colvars that have a value that lies in a particular interval
highest scalar HIGHEST the largest of the colvars
lowest scalar LOWEST the smallest of the colvars
sum scalar SUM the sum of the colvars
mean scalar MEAN the mean of the colvars

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
ATOMS atoms the atoms for which you would like to calculate the adjacency matrix
GROUPC atoms a group of atoms that must be summed over when calculating each element of the adjacency matrix

Further details and examples

Calculate the number of hydrogen bonds each hydrogen participates in using the HBPamm method

This shortcut action allows you to calculate the number of hydrogen bonds each of the atoms specified using the SITES keyword donates to its neighbours. The number of hydrogen bonds that a particular site donates is determined by using the PAMM tehcnique that is discussed in the articles from the bibliography below and in the documentation for the PAMM action

The following example shows how you can use this action to calculate how many hydrogen bonds each of the water moecules in a box of water donates to its neighbours.

Click on the labels of the actions for more information on what each action computes
tested on2.11
#SETTINGS INPUTFILES=regtest/pamm/rt-hbpamm/b3lyp.pamm
hyd: HBPAMM_SHCalculate the number of hydrogen bonds each hydrogen participates in using the HBPamm method This action is a shortcut. More details SITESThe list of atoms which can be part of a hydrogen bond=1-192:3 CLUSTERSthe name of the file that contains the definitions of all the kernels for PAMM=
regtest/pamm/rt-hbpamm/b3lyp.pamm
 Click here to see an extract from this file.
  
  ×  
FILE: regtest/pamm/rt-hbpamm/b3lyp.pamm
    
#! FIELDS height ptc ssc adc sigma_ptc_ptc sigma_ptc_ssc sigma_ptc_adc sigma_ssc_ptc sigma_ssc_ssc sigma_ssc_adc sigma_adc_ptc sigma_adc_ssc sigma_adc_adc
#! SET multivariate true
#! SET kerneltype gaussian
      7.62333341E-0002     -8.18288945E-0001      2.82463003E+0000      2.74063420E+0000      8.16250857E-0002     -6.73769671E-0002     -4.59932811E-0002     -6.73769671E-0002      6.75337422E-0002      4.53759149E-0002     -4.59932811E-0002      4.53759149E-0002      4.43189576E-0002 
      6.99310782E-0002      8.69642605E-0001      2.87365811E+0000      2.79326509E+0000      4.26992535E-0002      3.05953458E-0002      2.05388393E-0002      3.05953458E-0002      3.29012486E-0002      2.12273873E-0002      2.05388393E-0002      2.12273873E-0002      2.45196159E-0002 
      1.98671093E-0001     -2.27062808E+0000      4.25703566E+0000      2.78401408E+0000      7.98163641E-0002     -7.27264015E-0002     -1.99919283E-0002     -7.27264015E-0002      8.18886784E-0002      2.09866914E-0002     -1.99919283E-0002      2.09866914E-0002      4.62997869E-0002 
      1.45233007E-0002     -1.21470165E+0000      4.79894096E+0000      2.84314625E+0000      1.86259108E-0001     -2.27095842E-0002      2.85921248E-0002     -2.27095842E-0002      3.74404487E-0002     -3.26295559E-0003      2.85921248E-0002     -3.26295559E-0003      5.65919817E-0002 
      2.04518164E-0001      2.26156229E+0000      4.22597375E+0000      2.79821642E+0000      7.75379113E-0002      6.98466908E-0002      2.95665680E-0002      6.98466908E-0002      8.00913946E-0002      3.26640646E-0002      2.95665680E-0002      3.26640646E-0002      5.40779543E-0002 
      1.46258706E-0002      1.26722013E+0000      4.80633662E+0000      2.89897290E+0000      8.80357941E-0002      2.26981492E-0002      4.05790153E-0003      2.26981492E-0002      4.60485360E-0002     -7.70322510E-0003      4.05790153E-0003     -7.70322510E-0003      5.45100475E-0002 
      1.84562156E-0001     -2.60991008E+0000      4.59285310E+0000      4.03390174E+0000      1.51456600E-0001     -1.42734555E-0001     -1.17741061E-0001     -1.42734555E-0001      1.50000160E-0001      1.19653950E-0001     -1.17741061E-0001      1.19653950E-0001      2.01301812E-0001 
      2.87297679E-0002     -1.34664608E+0000      4.81762077E+0000      4.11037008E+0000      1.20169846E-0001     -2.40092647E-0002     -9.50215564E-0002     -2.40092647E-0002      3.53100140E-0002      4.17402875E-0002     -9.50215564E-0002      4.17402875E-0002      2.59240031E-0001 
      1.12880383E-0001      2.26335545E+0000      4.25751027E+0000      3.68162217E+0000      1.34662241E-0001      1.26724092E-0001      7.24910086E-0002      1.26724092E-0001      1.35760215E-0001      7.81381697E-0002      7.24910086E-0002      7.81381697E-0002      1.13119071E-0001 
      2.86798480E-0002      1.33616209E+0000      4.85052180E+0000      4.23465934E+0000      1.80874139E-0001      3.35404961E-0002      1.71858062E-0001      3.35404961E-0002      3.57517317E-0002      5.62338216E-0002      1.71858062E-0001      5.62338216E-0002      3.56622291E-0001 
      6.66450035E-0002      2.74946369E+0000      4.74656373E+0000      4.24763632E+0000      2.54371954E-0002      1.64469606E-0002      4.36734028E-0003      1.64469606E-0002      2.24742542E-0002      6.72714867E-0003      4.36734028E-0003      6.72714867E-0003      9.75985896E-0002 

  
 HYDROGENSThe list of hydrogen atoms that can form part of a hydrogen bond=2-192:3,3-192:3 MEAN calculate the mean of all the quantities
DUMPATOMSDump selected atoms on a file. More details ARGthe labels of vectors that should be output in the xyz file=hyd ATOMSthe atom indices whose positions you would like to print out=2-192:3,3-192:3 FILEfile on which to output coordinates; extension is automatically detected=hydrogens.xyz

The output here is an xyz with five columns. As explained in the documentation for DUMPATOMS, the first four columns are the usual columns that you would expect in an xyz file. The fifth column then contains the number of hydrogen bonds that each hydrogen atom participates in.

References

More information about how this action can be used is available in the following articles: - G. A. Tribello, F. Giberti, G. C. Sosso, M. Salvalaglio, M. Parrinello, Analyzing and Driving Cluster Formation in Atomistic Simulations. Journal of Chemical Theory and Computation. 13, 1317–1327 (2017) - P. Gasparotto, M. Ceriotti, Recognizing molecular patterns by machine learning: An agnostic structural definition of the hydrogen bond. The Journal of Chemical Physics. 141 (2014) - P. Gasparotto, R. H. Meißner, M. Ceriotti, Recognizing Local and Global Structural Motifs at the Atomic Scale. Journal of Chemical Theory and Computation. 14, 486–498 (2018)

Syntax

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

Keyword Type Default Description
ATOMS input none the atoms for which you would like to calculate the adjacency matrix
GROUPC input none a group of atoms that must be summed over when calculating each element of the adjacency matrix
NL_CUTOFF compulsory 0.0 The cutoff for the neighbor list
NL_STRIDE compulsory 1 The frequency with which we are updating the atoms in the neighbor list
ORDER compulsory dah the order in which the groups are specified in the input
CLUSTERS compulsory none the name of the file that contains the definitions of all the kernels for PAMM
REGULARISE compulsory 0.001 don't allow the denominator to be smaller then this value
GAUSS_CUTOFF compulsory 6.25 the cutoff at which to stop evaluating the kernel function is set equal to sqrt(2x)(max(adc)+cov(adc))
HYDROGENS compulsory none The list of hydrogen atoms that can form part of a hydrogen bond
SERIAL optional false do the calculation in serial
NOPBC optional false don't use pbc
SITES optional not used The list of atoms which can be part of a hydrogen bond
DONORS optional not used The list of atoms which can donate a hydrogen bond
ACCEPTORS optional not used The list of atoms which can accept a hydrogen bond
LESS_THAN optional not used calculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN.
MORE_THAN optional not used calculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.
ALT_MIN optional not used calculate the minimum value
MIN optional not used calculate the minimum value
MAX optional not used calculate the maximum value
BETWEEN optional not used calculate the number of values that are within a certain range. Options for this keyword are explained in the documentation for BETWEEN.
HIGHEST optional false this flag allows you to recover the highest of these variables
HISTOGRAM optional not used calculate a discretized histogram of the distribution of values
LOWEST optional false this flag allows you to recover the lowest of these variables
SUM optional false calculate the sum of all the quantities
MEAN optional false calculate the mean of all the quantities