Action: CONTACTMAP
| Module | colvar |
|---|---|
| Description | Usage |
| Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. |   |
| output value | type |
| the sum of all the switching function on all the distances | scalar |
Output components
This action calculates the values in the following table. 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 | Description |
|---|---|---|
| contact | scalar | By not using SUM or CMDIST each contact will be stored in a component |
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 involved in each of the contacts you wish to calculate |
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:
- M. Bonomi, D. Branduardi, F. L. Gervasio, M. Parrinello, The Unfolded Ensemble and Folding Mechanism of the C-Terminal GB1 β-Hairpin. Journal of the American Chemical Society. 130, 13938–13944 (2008)
- R. B. Best, G. Hummer, W. A. Eaton, Native contacts determine protein folding mechanisms in atomistic simulations. Proceedings of the National Academy of Sciences. 110, 17874–17879 (2013)
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 involved in each of the contacts you wish to calculate |
| SWITCH | compulsory | none | The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN. |
| NUMERICAL_DERIVATIVES | optional | false | calculate the derivatives for these quantities numerically |
| NOPBC | optional | false | ignore the periodic boundary conditions when calculating distances |
| REFERENCE | optional | not used | A reference value for a given contact, by default is 0 |
| WEIGHT | optional | not used | A weight value for a given contact, by default is 1 |
| SUM | optional | false | calculate the sum of all the contacts in the input |
| CMDIST | optional | false | calculate the distance with respect to the provided reference contact map |
| SERIAL | optional | false | Perform the calculation in serial - for debug purpose |