| This is part of the symfunc module |
| It is only available if you configure PLUMED with ./configure –enable-modules=symfunc . Furthermore, this feature is still being developed so take care when using it and report any problems on the mailing list. |
Calculate the SMAC order parameter for a set of molecules
- Examples
- Glossary of keywords and components
- Description of components
| Quantity | Description |
| .#!value | the value of the smac parameter for each of the input molecules |
In addition the following quantities can be calculated by employing the keywords listed below
| Quantity | Keyword | Description |
| lessthan | LESS_THAN | the number of colvars that have a value less than a threshold |
| morethan | MORE_THAN | the number of colvars that have a value more than a threshold |
| altmin | ALT_MIN | the minimum value of the cv |
| min | MIN | the minimum colvar |
| max | MAX | the maximum colvar |
| between | BETWEEN | the number of colvars that have a value that lies in a particular interval |
| highest | HIGHEST | the largest of the colvars |
| lowest | LOWEST | the smallest of the colvars |
| sum | SUM | the sum of the colvars |
| mean | MEAN | the mean of the colvars |
- Options
| HIGHEST | ( default=off ) this flag allows you to recover the highest of these variables. |
| LOWEST | ( default=off ) this flag allows you to recover the lowest of these variables. |
| SUM | ( default=off ) calculate the sum of all the quantities. |
| MEAN | ( default=off ) calculate the mean of all the quantities.
|
| SPECIES | |
| SPECIESA | |
| SPECIESB | |
| SWITCH | This keyword is used if you want to employ an alternative to the continuous swiching function defined above. The following provides information on the switchingfunction that are available. When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords. |
| KERNEL | The kernels used in the function of the angle. You can use multiple instances of this keyword i.e. KERNEL1, KERNEL2, KERNEL3... |
| SWITCH_COORD | This keyword is used to define the coordination switching function. |
| LESS_THAN | calculate the number of variables that are less than a certain target value. This quantity is calculated using \(\sum_i \sigma(s_i)\), where \(\sigma(s)\) is a switchingfunction.. You can use multiple instances of this keyword i.e. LESS_THAN1, LESS_THAN2, LESS_THAN3... |
| MORE_THAN | calculate the number of variables that are more than a certain target value. This quantity is calculated using \(\sum_i 1 - \sigma(s_i)\), where \(\sigma(s)\) is a switchingfunction.. You can use multiple instances of this keyword i.e. MORE_THAN1, MORE_THAN2, MORE_THAN3... |
| ALT_MIN | calculate the minimum value. To make this quantity continuous the minimum is calculated using \( \textrm{min} = -\frac{1}{\beta} \log \sum_i \exp\left( -\beta s_i \right) \) The value of \(\beta\) in this function is specified using (BETA= \(\beta\)). |
| MIN | calculate the minimum value. To make this quantity continuous the minimum is calculated using \( \textrm{min} = \frac{\beta}{ \log \sum_i \exp\left( \frac{\beta}{s_i} \right) } \) The value of \(\beta\) in this function is specified using (BETA= \(\beta\)) |
| MAX | calculate the maximum value. To make this quantity continuous the maximum is calculated using \( \textrm{max} = \beta \log \sum_i \exp\left( \frac{s_i}{\beta}\right) \) The value of \(\beta\) in this function is specified using (BETA= \(\beta\)) |
| BETWEEN | calculate the number of values that are within a certain range. These quantities are calculated using kernel density estimation as described on histogrambead.. You can use multiple instances of this keyword i.e. BETWEEN1, BETWEEN2, BETWEEN3... |
| HISTOGRAM | calculate a discretized histogram of the distribution of values. This shortcut allows you to calculates NBIN quantites like BETWEEN. |
1.8.17