TORSIONS
This is part of the multicolvar module

Calculate whether or not a set of torsional angles are within a particular range.

Examples

The following provides an example of the input for the TORSIONS command

Click on the labels of the actions for more information on what each action computes
tested on v2.9
ab: TORSIONS ...
   
ATOMS1
the atoms involved in each of the torsion angles you wish to calculate. 
=168,170,172,188 
   
ATOMS2
the atoms involved in each of the torsion angles you wish to calculate. 
=170,172,188,190 
   
ATOMS3
the atoms involved in each of the torsion angles you wish to calculate. 
=188,190,192,230 
   
BETWEEN
calculate the number of values that are within a certain range. 
={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}  
   
...
PRINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=ab.* 
FILE
the name of the file on which to output these quantities 
=colvar 
STRIDE
compulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output 
=10

Writing out the atoms involved in all the torsion angles in this way can be rather tedious. Thankfully if you are working with protein you can avoid this by using the MOLINFO command. PLUMED uses the pdb file that you provide to this command to learn about the topology of the protein molecule. This means that you can specify torsion angles using the following syntax:

Click on the labels of the actions for more information on what each action computes
tested on v2.9
#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
MOLINFO 
MOLTYPE
compulsory keyword ( default=protein )
what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA
are compatible 
=protein 
STRUCTURE
compulsory keyword 
a file in pdb format containing a reference structure. 
=myprotein.pdb 
ab: TORSIONS ...
   
ATOMS1
the atoms involved in each of the torsion angles you wish to calculate. 
=@phi-3 
   
ATOMS2
the atoms involved in each of the torsion angles you wish to calculate. 
=@psi-3 
   
ATOMS3
the atoms involved in each of the torsion angles you wish to calculate. 
=@phi-4 
   
BETWEEN
calculate the number of values that are within a certain range. 
={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}  
   
...
PRINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=ab.* 
FILE
the name of the file on which to output these quantities 
=colvar 
STRIDE
compulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output 
=10

Here, @phi-3 tells plumed that you would like to calculate the \(\phi\) angle in the third residue of the protein. Similarly @psi-4 tells plumed that you want to calculate the \(\psi\) angle of the fourth residue of the protein.

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
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.
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 provide the indices of four 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...
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

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...