	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.

Number of HBPAMM hydrogen bonds formed by each hydrogen atom in the system

Examples

Glossary of keywords and components

Description of components

When the label of this action is used as the input for a second you are not referring to a scalar quantity as you are in regular collective variables. The label is used to reference the full set of quantities calculated by the action. This is usual when using MultiColvar functions. Generally when doing this the previously calculated multicolvar will be referenced using the DATA keyword rather than ARG.

This Action can be used to calculate the following scalar quantities directly. These quantities are calculated by employing the keywords listed below. These quantities can then be referenced elsewhere in the input file by using this Action's label followed by a dot and the name of the quantity. Some of them can be calculated multiple times with different parameters. In this case the quantities calculated can be referenced elsewhere in the input by using the name of the quantity followed by a numerical identifier e.g. label.lessthan-1, label.lessthan-2 etc. When doing this and, for clarity we have made it so that the user can set a particular label for each of the components. As such by using the LABEL keyword in the description of the keyword input you can customize the component name

Quantity	Keyword	Description
altmin	ALT_MIN	the minimum value. This is calculated using the formula described in the description of the keyword so as to make it continuous.
between	BETWEEN	the number/fraction of values within a certain range. This is calculated using one of the formula described in the description of the keyword so as to make it continuous. You can calculate this quantity multiple times using different parameters.
highest	HIGHEST	the highest of the quantities calculated by this action
lessthan	LESS_THAN	the number of values less than a target value. This is calculated using one of the formula described in the description of the keyword so as to make it continuous. You can calculate this quantity multiple times using different parameters.
lowest	LOWEST	the lowest of the quantities calculated by this action
max	MAX	the maximum value. This is calculated using the formula described in the description of the keyword so as to make it continuous.
mean	MEAN	the mean value. The output component can be referred to elsewhere in the input file by using the label.mean
min	MIN	the minimum value. This is calculated using the formula described in the description of the keyword so as to make it continuous.
moment	MOMENTS	the central moments of the distribution of values. The second moment would be referenced elsewhere in the input file using label.moment-2, the third as label.moment-3, etc.
morethan	MORE_THAN	the number of values more than a target value. This is calculated using one of the formula described in the description of the keyword so as to make it continuous. You can calculate this quantity multiple times using different parameters.
sum	SUM	the sum of values

The atoms involved can be specified using

HYDROGENS

The list of hydrogen atoms that can form part of a hydrogen bond. The atoms must be specified using a comma separated list.

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 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

Or alternatively by using

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

Compulsory keywords

CLUSTERS	the name of the file that contains the definitions of all the kernels for PAMM You can use multiple instances of this keyword i.e. CLUSTERS1, CLUSTERS2, CLUSTERS3...
REGULARISE	( default=0.001 ) don't allow the denominator to be smaller then this value

Options

NUMERICAL_DERIVATIVES	( default=off ) calculate the derivatives for these quantities numerically
NOPBC	( default=off ) ignore the periodic boundary conditions when calculating distances
SERIAL	( default=off ) do the calculation in serial. Do not use MPI
LOWMEM	( default=off ) lower the memory requirements
TIMINGS	( default=off ) output information on the timings of the various parts of the calculation
MEAN	take the mean of these variables. The final value can be referenced using label.mean. You can use multiple instances of this keyword i.e. MEAN1, MEAN2, MEAN3... The corresponding values are then referenced using label.mean-1, label.mean-2, label.mean-3...
MORE_THAN	calculate the number of variables more than a certain target value. This quantity is calculated using \(\sum_i 1.0 - \sigma(s_i)\), where \(\sigma(s)\) is a switchingfunction. The final value can be referenced using label.morethan. You can use multiple instances of this keyword i.e. MORE_THAN1, MORE_THAN2, MORE_THAN3... The corresponding values are then referenced using label.morethan-1, label.morethan-2, label.morethan-3...
LESS_THAN	calculate the number of variables less than a certain target value. This quantity is calculated using \(\sum_i \sigma(s_i)\), where \(\sigma(s)\) is a switchingfunction. The final value can be referenced using label.lessthan. You can use multiple instances of this keyword i.e. LESS_THAN1, LESS_THAN2, LESS_THAN3... The corresponding values are then referenced using label.lessthan-1, label.lessthan-2, label.lessthan-3...
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= \(\beta\)) The final value can be referenced using label.max. You can use multiple instances of this keyword i.e. MAX1, MAX2, MAX3... The corresponding values are then referenced using label.max-1, label.max-2, label.max-3...
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= \(\beta\)) The final value can be referenced using label.min. You can use multiple instances of this keyword i.e. MIN1, MIN2, MIN3... The corresponding values are then referenced using label.min-1, label.min-2, label.min-3...
BETWEEN	calculate the number of values that are within a certain range. These quantities are calculated using kernel density estimation as described on histogrambead. The final value can be referenced using label.between. You can use multiple instances of this keyword i.e. BETWEEN1, BETWEEN2, BETWEEN3... The corresponding values are then referenced using label.between-1, label.between-2, label.between-3...
HISTOGRAM	calculate how many of the values fall in each of the bins of a histogram. This shortcut allows you to calculates NBIN quantities like BETWEEN. The final value can be referenced using label.histogram. You can use multiple instances of this keyword i.e. HISTOGRAM1, HISTOGRAM2, HISTOGRAM3... The corresponding values are then referenced using label.histogram-1, label.histogram-2, label.histogram-3...
MOMENTS	calculate the moments of the distribution of collective variables. The mth moment of a distribution is calculated using \(\frac{1}{N} \sum_{i=1}^N ( s_i - \overline{s} )^m \), where \(\overline{s}\) is the average for the distribution. The moments keyword takes a lists of integers as input or a range. Each integer is a value of \(m\). The final calculated values can be referenced using moment- \(m\). You can use the COMPONENT keyword in this action but the syntax is slightly different. If you would like the second and third moments of the third component you would use MOMENTS={COMPONENT=3 MOMENTS=2-3}. The moments would then be referred to using the labels moment-3-2 and moment-3-3. This syntax is also required if you are using numbered MOMENT keywords i.e. MOMENTS1, MOMENTS2...
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= \(\beta\)). The final value can be referenced using label.altmin. You can use multiple instances of this keyword i.e. ALT_MIN1, ALT_MIN2, ALT_MIN3... The corresponding values are then referenced using label.altmin-1, label.altmin-2, label.altmin-3...
LOWEST	this flag allows you to recover the lowest of these variables. The final value can be referenced using label.lowest
HIGHEST	this flag allows you to recover the highest of these variables. The final value can be referenced using label.highest
SUM	calculate the sum of all the quantities. The final value can be referenced using label.sum. You can use multiple instances of this keyword i.e. SUM1, SUM2, SUM3... The corresponding values are then referenced using label.sum-1, label.sum-2, label.sum-3...