Shortcut: PAMM
| Module | pamm |
|---|---|
| Description | Usage |
| Probabilistic analysis of molecular motifs. |   |
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 |
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:
- 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 |
|---|---|---|---|
| ARG | compulsory | none | the vectors from which the pamm coordinates are calculated |
| CLUSTERS | compulsory | none | the name of the file that contains the definitions of all the clusters |
| REGULARISE | compulsory | 0.001 | don’t allow the denominator to be smaller then this value |
| KERNELS | compulsory | all | which kernels are we computing the PAMM values for |
| 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 |