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

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}  
   
... You cannot view the components that are calculated by each action for this input file. Sorry 
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  You cannot view the components that are calculated by each action for this input file. Sorry 

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

#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  You cannot view the components that are calculated by each action for this input file. Sorry 
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}  
   
... You cannot view the components that are calculated by each action for this input file. Sorry 
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  You cannot view the components that are calculated by each action for this input file. Sorry 

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.