Shortcut: TORSIONS

Module	multicolvar
Description	Usage
Calculate whether or not a set of torsional angles are within a particular range.
output value	type
the TORSION for each set of three atoms that were specified	vector

Deprecated

This action has been deprecated and is no longer supported. Use TORSION instead.

Details and examples

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

This shortcut action allows you to calculate function of a distribution of torsions and reproduces the syntax in older PLUMED versions. If you look at the example inputs below you can see how the new syntax operates. We would strongly encourage you to use the newer syntax as it offers greater flexibility.

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

abThe TORSIONS action with label ab calculates the following quantities:
 Quantity   
 Type   
 Description  
ab
vector
the TORSION for each set of three atoms that were specified
ab_between
scalar
the number of colvars that have a value that lies in a particular interval: TORSIONSCalculate whether or not a set of torsional angles are within a particular range. This action is a shortcut. More details ...
  ATOMS1the four atoms involved in the torsional angle=168,170,172,188
  ATOMS2the four atoms involved in the torsional angle=170,172,188,190
  ATOMS3the four atoms involved in the torsional angle=188,190,192,230
  BETWEENcalculate the number of values that are within a certain range. Options for this keyword are explained in the documentation for BETWEEN.={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}
...
# PLUMED interprets the command:
# ab: TORSIONS ...
#   ATOMS1=168,170,172,188
#   ATOMS2=170,172,188,190
#   ATOMS3=188,190,192,230
#   BETWEEN={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}
# ...
# as follows (Click the red comment above to revert to the short version of the input):
abThe TORSION action with label ab calculates the following quantities:
 Quantity   
 Type   
 Description  
ab
vector
the TORSION for each set of specified atoms: TORSIONCalculate one or multiple torsional angles. More details  ATOMS1the four atoms involved in the torsional angle=168,170,172,188 ATOMS2the four atoms involved in the torsional angle=170,172,188,190 ATOMS3the four atoms involved in the torsional angle=188,190,192,230
ab_btThe BETWEEN action with label ab_bt calculates the following quantities:
 Quantity   
 Type   
 Description  
ab_bt
vector
the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors: BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=ab SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}
ab_betweenThe SUM action with label ab_between calculates the following quantities:
 Quantity   
 Type   
 Description  
ab_between
scalar
the SUM of the elements in the input value: SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=ab_bt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=ab.* FILEthe name of the file on which to output these quantities=colvar STRIDE the frequency with which the quantities of interest should be output=10

The input above calculates how many of torsion angles for the three groups of atoms that have been specified are between 0 and $\pi$.

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
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details MOLTYPE what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible=protein STRUCTUREa file in pdb format containing a reference structure=
regtest/basic/rt32/helix.pdb
 Click here to see an extract from this file.
  
  ×  
FILE: regtest/basic/rt32/helix.pdb
    
ATOM      1 HH31 ACE     1      -9.105  -2.402  21.804  0.00  0.00            
ATOM      2  CH3 ACE     1      -8.930  -3.352  22.308  0.00  0.00            
ATOM      3 HH32 ACE     1      -9.504  -3.501  23.223  0.00  0.00            
ATOM      4 HH33 ACE     1      -9.067  -4.173  21.604  0.00  0.00            
ATOM      5  C   ACE     1      -7.450  -3.303  22.659  0.00  0.00            
...
ATOM    129  CH3 NME    14      -1.690  -7.089  20.487  0.00  0.00            
ATOM    130 HH31 NME    14      -1.873  -6.629  21.459  0.00  0.00            
ATOM    131 HH32 NME    14      -1.152  -6.284  19.986  0.00  0.00            
ATOM    132 HH33 NME    14      -1.135  -8.020  20.602  0.00  0.00            
END
  
The MOLINFO action with label  calculates somethingTORSIONSCalculate whether or not a set of torsional angles are within a particular range. This action is a shortcut. More details ...
ATOMS1the four atoms involved in the torsional angle=@phi-3the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information. 
ATOMS2the four atoms involved in the torsional angle=@psi-3the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information. 
ATOMS3the four atoms involved in the torsional angle=@phi-4the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information. 
BETWEENcalculate the number of values that are within a certain range. Options for this keyword are explained in the documentation for BETWEEN.={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}
LABELa label for the action so that its output can be referenced in the input to other actions=abThe TORSIONS action with label ab calculates the following quantities:
 Quantity   
 Type   
 Description  
ab
vector
the TORSION for each set of three atoms that were specified
ab_between
scalar
the number of colvars that have a value that lies in a particular interval
... TORSIONS
# PLUMED interprets the command:
# TORSIONS ...
# ATOMS1=@phi-3
# ATOMS2=@psi-3
# ATOMS3=@phi-4
# BETWEEN={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}
# LABEL=ab
# ... TORSIONS
# as follows (Click the red comment above to revert to the short version of the input):
abThe TORSION action with label ab calculates the following quantities:
 Quantity   
 Type   
 Description  
ab
vector
the TORSION for each set of specified atoms: TORSIONCalculate one or multiple torsional angles. More details  ATOMS1the four atoms involved in the torsional angle=@phi-3the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information.  ATOMS2the four atoms involved in the torsional angle=@psi-3the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information.  ATOMS3the four atoms involved in the torsional angle=@phi-4the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information. 
ab_btThe BETWEEN action with label ab_bt calculates the following quantities:
 Quantity   
 Type   
 Description  
ab_bt
vector
the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors: BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=ab SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}
ab_betweenThe SUM action with label ab_between calculates the following quantities:
 Quantity   
 Type   
 Description  
ab_between
scalar
the SUM of the elements in the input value: SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=ab_bt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=ab.* FILEthe name of the file on which to output these quantities=colvar STRIDE 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.

Input

The atoms that serve as the input for this action are specified using one or more of the keywords in the following table.

Keyword	Type	Description
ATOMS	atoms	the four atoms involved in the torsional angle

Output components

This action can calculate the values in the following table when the associated keyword is included in the input for the action. These values can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the value required from the list below.

Name	Type	Keyword	Description
lessthan	scalar	LESS_THAN	the number of colvars that have a value less than a threshold
morethan	scalar	MORE_THAN	the number of colvars that have a value more than a threshold
altmin	scalar	ALT_MIN	the minimum value of the cv
min	scalar	MIN	the minimum colvar
max	scalar	MAX	the maximum colvar
between	scalar	BETWEEN	the number of colvars that have a value that lies in a particular interval
highest	scalar	HIGHEST	the largest of the colvars
lowest	scalar	LOWEST	the smallest of the colvars
sum	scalar	SUM	the sum of the colvars
mean	scalar	MEAN	the mean of the colvars

Full list of keywords

The following table describes the keywords and options that can be used with this action

Keyword	Type	Default	Description
ATOMS	input	none	the four atoms involved in the torsional angle
LESS_THAN	optional	not used	calculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN.
MORE_THAN	optional	not used	calculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.
ALT_MIN	optional	not used	calculate the minimum value
MIN	optional	not used	calculate the minimum value
MAX	optional	not used	calculate the maximum value
BETWEEN	optional	not used	calculate the number of values that are within a certain range. Options for this keyword are explained in the documentation for BETWEEN.
HIGHEST	optional	not used	this flag allows you to recover the highest of these variables
HISTOGRAM	optional	not used	calculate a discretized histogram of the distribution of values
LOWEST	optional	not used	this flag allows you to recover the lowest of these variables
SUM	optional	not used	calculate the sum of all the quantities
MEAN	optional	not used	calculate the mean of all the quantities