Action: S2CM
| Module | s2cm |
|---|---|
| Description | Usage |
| S2 contact model CV. |   |
| output value | type |
| the value of the CV | scalar |
Details and examples
S2 contact model CV.
This CV was used in the first paper cited below. It is based on NH order parameter from the second paper cited below and the methyl order parameter from the third. Input parameters can be found in the relevant papers.
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 |
|---|---|---|
| METHYL_ATOM | atoms | the methyl carbon atom of the residue (i) |
| NH_ATOMS | atoms | the hydrogen atom of the NH group of the residue (i) and carbonyl oxygen of the preceding residue (i-1) |
| HEAVY_ATOMS | atoms | the heavy atoms to be included in the calculation |
Full list of keywords
The following table describes the keywords and options that can be used with this action
| Keyword | Type | Default | Description |
|---|---|---|---|
| METHYL_ATOMThis keyword do not have examples | input | none | the methyl carbon atom of the residue (i) |
| NH_ATOMSThis keyword do not have examples | input | none | the hydrogen atom of the NH group of the residue (i) and carbonyl oxygen of the preceding residue (i-1) |
| HEAVY_ATOMSThis keyword do not have examples | input | none | the heavy atoms to be included in the calculation |
| R_EFFThis keyword do not have examples | compulsory | none | the effective distance, r_eff in the equation, given in nm |
| PREFACTOR_AThis keyword do not have examples | compulsory | none | the prefactor, a in the equation |
| EXPONENT_BThis keyword do not have examples | compulsory | none | the exponent, b in the equation |
| OFFSET_CThis keyword do not have examples | compulsory | none | the offset, c in the equation |
| N_IThis keyword do not have examples | compulsory | none | n_i in the equation |
| NUMERICAL_DERIVATIVESThis keyword do not have examples | optional | false | calculate the derivatives for these quantities numerically |
| NOPBCThis keyword do not have examples | optional | false | ignore the periodic boundary conditions when calculating distances |
| SERIALThis keyword do not have examples | optional | false | Perform the calculation in serial - for debug purpose |
| NLISTThis keyword do not have examples | optional | false | Use a neighbour list to speed up the calculation |
| NL_CUTOFFThis keyword do not have examples | optional | not used | The cutoff for the neighbour list |
| NL_STRIDEThis keyword do not have examples | optional | not used | The frequency with which we are updating the atoms in the neighbour list |
| R_SHIFTThis keyword do not have examples | optional | not used | shift all distances by given amount |
References
More information about how this action can be used is available in the following articles:
- F. Palazzesi, O. Valsson, M. Parrinello, Conformational Entropy as Collective Variable for Proteins. The Journal of Physical Chemistry Letters. 8, 4752–4756 (2017)
- F. Zhang, R. Brüschweiler, Contact Model for the Prediction of NMR N−H Order Parameters in Globular Proteins. Journal of the American Chemical Society. 124, 12654–12655 (2002)
- D. Ming, R. Brüschweiler, Prediction of methyl-side Chain Dynamics in Proteins. Journal of Biomolecular NMR. 29, 363–368 (2004)