XZTORSIONS
 This is part of the multicolvar module

Calculate the torsional angle around the x axis from the positive z direction.

Examples

The following input tells plumed to calculate the angle around the x direction between the positive z-axis and the vector connecting atom 3 to atom 5 and the angle around the x direction between the positive z direction and the vector connecting atom 1 to atom 2. The minimum of these two quantities is then output

Click on the labels of the actions for more information on what each action computes
d1: XZTORSIONS ATOMS1the atoms involved in each of the torsion angles you wish to calculate. =3,5 ATOMS2the atoms involved in each of the torsion angles you wish to calculate. =1,2 BETWEENcalculate the number of values that are within a certain range. ={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}
PRINT ARGthe input for this action is the scalar output from one or more other actions. =d1.*


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 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.
The atoms involved can be specified using
 ATOMS the atoms involved in each of the torsion angles you wish to calculate. Keywords like ATOMS1, ATOMS2, ATOMS3,... should be listed and one torsion will be calculated for each ATOM keyword you specify (all ATOM keywords should specify the indices of two atoms). The eventual number of quantities calculated by this action will depend on what functions of the distribution you choose to calculate. You can use multiple instances of this keyword i.e. ATOMS1, ATOMS2, ATOMS3...
Or alternatively by using
 GROUP Calculate the distance between each distinct pair of atoms in the group
Or alternatively by using
 GROUPA Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB. This must be used in conjunction with GROUPB. GROUPB Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB. This must be used in conjunction with GROUPA.
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 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... 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... 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... 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... 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 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... SWITCH A switching function that ensures that only angles are only computed when atoms are within are within a certain fixed cutoff. The following provides information on the switchingfunction that are available.