| This is part of the pamm module |
| It is only available if you configure PLUMED with ./configure –enable-modules=pamm . Furthermore, this feature is still being developed so take care when using it and report any problems on the mailing list. |
Calculate the number of hydrogen bonds each acceptor participates in using the HBPamm method
- Examples
- Glossary of keywords and components
- Description of components
By default the value of the calculated quantity can be referenced elsewhere in the input file by using the label of the action. Alternatively this Action can be used to calculate the following quantities by employing the keywords listed below. These quantities can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the quantity required from the list below.
| Quantity | Description |
| .#!value | a vector specifiying the number of hydrogen bonds each of the specified atoms participates within |
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 |
- The atoms involved can be specified using
| ATOMS | the atoms for which you would like to calculate the adjacency matrix. This is a depracated syntax that is equivalent to GROUP. You are strongly recommened to use GROUP instead of ATOMS. |
- Or alternatively by using
- Compulsory keywords
| NL_CUTOFF | ( default=0.0 ) The cutoff for the neighbor list. A value of 0 means we are not using a neighbor list |
| NL_STRIDE | ( default=1 ) The frequency with which we are updating the atoms in the neighbor list |
| ORDER | ( default=dah ) the order in which the groups are specified in the input. Can be dah (donor/acceptor/hydrogens), adh (acceptor/donor/hydrogens) or hda (hydrogens/donor/hydrogens |
| CLUSTERS | the name of the file that contains the definitions of all the kernels for PAMM |
| REGULARISE | ( default=0.001 ) don't allow the denominator to be smaller then this value |
| GAUSS_CUTOFF | ( default=6.25 ) the cutoff at which to stop evaluating the kernel function is set equal to sqrt(2*x)*(max(adc)+cov(adc)) |
| HYDROGENS | The list of hydrogen atoms that can form part of a hydrogen bond. The atoms must be specified using a comma separated list, an index range or by using a GROUP |
- Options
| SERIAL | ( default=off ) do the calculation in serial. Do not parallelize |
| NOPBC | ( default=off ) don't use pbc |
| 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.
|
| SITES | The list of atoms which can be part of a hydrogen bond. When this command is used the set of atoms that can donate a hydrogen bond is assumed to be the same as the set of atoms that can form hydrogen bonds. The atoms involved must be specifiedas a list of labels of MultiColvar or labels of a MultiColvar functions actions. If you would just like to use the atomic positions you can use a DENSITY command to specify a group of atoms. Specifying your atomic positions using labels of other MultiColvar or MultiColvar functions commands is useful, however, as you can then exploit a much wider variety of functions of the contact matrix as described in Exploiting contact matrices |
| DONORS | The list of atoms which can donate a hydrogen bond. The atoms involved must be specified as a list of labels of MultiColvar or labels of a MultiColvar functions actions. If you would just like to use the atomic positions you can use a DENSITY command to specify a group of atoms. Specifying your atomic positions using labels of other MultiColvar or MultiColvar functions commands is useful, however, as you can then exploit a much wider variety of functions of the contact matrix as described in Exploiting contact matrices |
| ACCEPTORS | The list of atoms which can accept a hydrogen bond. The atoms involved must be specified as a list of labels of MultiColvar or labels of a MultiColvar functions actions. If you would just like to use the atomic positions you can use a DENSITY command to specify a group of atoms. Specifying your atomic positions using labels of other MultiColvar or MultiColvar functions commands is useful, however, as you can then exploit a much wider variety of functions of the contact matrix as described in Exploiting contact matrices |
| 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