Action: HBPAMM_SD
| Module | pamm |
|---|---|
| Description | Usage |
| Calculate the number of hydrogen bonds each donor participates in using the HBPamm method |   |
| 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
Text from manual goes here
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 |