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 master
ab: TORSIONS ...
   
ATOMS1
could not find this keyword
=168,170,172,188
ATOMS2
could not find this keyword
=170,172,188,190
ATOMS3
could not find this keyword
=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
compulsory keyword the labels of the values that you would like to print to the file
=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 master
#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
could not find this keyword
=@phi-3
ATOMS2
could not find this keyword
=@psi-3
ATOMS3
could not find this keyword
=@phi-4
BETWEEN
calculate the number of values that are within a certain range.
={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1} ... PRINT
ARG
compulsory keyword the labels of the values that you would like to print to the file
=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
Quantity Description
.#!value the TORSION for each set of three atoms that were specified

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.

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.