ZDISTANCES

This is part of the multicolvar module

Calculate the z components of the vectors connecting one or many pairs of atoms. You can then calculate functions of the distribution of values such as the minimum, the number less than a certain quantity and so on.

Examples

The following input tells plumed to calculate the z-component of the vector connecting atom 3 to atom 5 and the z-component of the vector connecting atom 1 to atom 2. The minimum of these two quantities is then printed

Click on the labels of the actions for more information on what each action computes

contract shortcuts

d1: ZDISTANCES ATOMS1the pairs of atoms that you would like to calculate the angles for. =3,5 ATOMS2the pairs of atoms that you would like to calculate the angles for. =1,2 MINcalculate the minimum value. ={BETA=0.1}  The ZDISTANCES action with label d1 calculates the following quantities:

 Quantity   
 Description  
d1.x
the x-components of the distance vectors
d1.y
the y-components of the distance vectors
d1.z
the z-components of the distance vectors


PRINT ARGthe input for this action is the scalar output from one or more other actions. =d1.min The PRINT action with label 

d1_vatom1: CENTER ATOMSthe group of atoms that you are calculating the Gyration Tensor for. =3,5 The CENTER action with label d1_vatom1 calculates the following quantities:

 Quantity   
 Description  
d1_vatom1.x
 (See also PRINT).
The following input tells plumed to calculate the z-component of the vector connecting atom 3 to atom 5 and the z-component of the vector connecting atom 1 to atom 2. The number of values that are less than 0.1nm is then printed to a file. 
 Click on the labels of the actions for more information on what each action computes 
contract shortcuts




d1: ZDISTANCES ATOMS1the pairs of atoms that you would like to calculate the angles for. =3,5 ATOMS2the pairs of atoms that you would like to calculate the angles for. =1,2 LESS_THANcalculate the number of variables that are less than a certain target value. ={RATIONAL R_0=0.1}  The ZDISTANCES action with label d1 calculates the following quantities:

 Quantity   
 Description  
d1.x
the x-components of the distance vectors
d1.y
the y-components of the distance vectors
d1.z
the z-components of the distance vectors


PRINT ARGthe input for this action is the scalar output from one or more other actions. =d1.lessthan The PRINT action with label 


d1_vatom1: CENTER ATOMSthe group of atoms that you are calculating the Gyration Tensor for. =3,5 The CENTER action with label d1_vatom1 calculates the following quantities:

 Quantity   
 Description  
d1_vatom1.x
 (See also PRINT switchingfunction).
The following input tells plumed to calculate the z-components of all the distinct vectors that can be created between atoms 1, 2 and 3 (i.e. the vectors between atoms 1 and 2, atoms 1 and 3 and atoms 2 and 3). The average of these quantities is then calculated. 
 Click on the labels of the actions for more information on what each action computes 
contract shortcuts




d1: ZDISTANCES GROUPCalculate the distance between each distinct pair of atoms in the group =1-3 MEAN( default=off ) calculate the mean of all the quantities.  The ZDISTANCES action with label d1 calculates the following quantities:

 Quantity   
 Description  
d1.x
the x-components of the distance vectors
d1.y
the y-components of the distance vectors
d1.z
the z-components of the distance vectors


PRINT ARGthe input for this action is the scalar output from one or more other actions. =d1.mean The PRINT action with label 


d1: DISTANCE COMPONENTS( default=off ) calculate the x, y and z components of the distance separately and
store them as label.x,  ATOMS1the pair of atom that we are calculating the distance between. =2,1 ATOMS2the pair of atom that we are calculating the distance between. =3,1 ATOMS3the pair of atom that we are calculating the distance between. =3,2 The DISTANCE action with label d1 calculates the following quantities:

 Quantity   
 Description  
d1.x
the x-component of the vector connecting the two atoms
d1.y
the y-component of the vector connecting the two atoms
d1.z
the z-component of the vector connecting the two atoms


d1_mean: MEAN ARGthe input to this function. =d1.z PERIODICcompulsory keyword 
if the output of your function is periodic then you should specify the periodicity
of the function. =NO The MEAN action with label d1_mean calculates a single scalar value
PRINT ARGthe input for this action is the scalar output from one or more other actions. =d1.mean The PRINT action with label 


 (See also PRINT)
The following input tells plumed to calculate all the vectors connecting the the atoms in GROUPA to the atoms in GROUPB. In other words the vector between atoms 1 and 2 and the vector between atoms 1 and 3. The number of values more than 0.1 is then printed to a file. 
 Click on the labels of the actions for more information on what each action computes 
contract shortcuts




d1: ZDISTANCES GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB.
=1 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB.
=2,3 MORE_THANcalculate the number of variables that are more than a certain target value. ={RATIONAL R_0=0.1}  The ZDISTANCES action with label d1 calculates the following quantities:

 Quantity   
 Description  
d1.x
the x-components of the distance vectors
d1.y
the y-components of the distance vectors
d1.z
the z-components of the distance vectors


PRINT ARGthe input for this action is the scalar output from one or more other actions. =d1.morethan The PRINT action with label 


d1: DISTANCE COMPONENTS( default=off ) calculate the x, y and z components of the distance separately and
store them as label.x,  ATOMS1the pair of atom that we are calculating the distance between. =1,2 ATOMS2the pair of atom that we are calculating the distance between. =1,3 The DISTANCE action with label d1 calculates the following quantities:

 Quantity   
 Description  
d1.x
the x-component of the vector connecting the two atoms
d1.y
the y-component of the vector connecting the two atoms
d1.z
the z-component of the vector connecting the two atoms


d1_mt: MORE_THAN ARGthe input to this function. =d1.z SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching
function defined above. =RATIONAL,R_0=0.1 The MORE_THAN action with label d1_mt
 (See also PRINT switchingfunction)
Glossary of keywords and components

Description of components



 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   

 x  
 COMPONENTS   
the x-components of the distance vectors   

 y  
 COMPONENTS   
the y-components of the distance vectors   

 z  
 COMPONENTS   
the z-components of the distance vectors   

The atoms involved can be specified 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.   

Or alternatively by using



 ATOMS  
the pairs of atoms that you would like to calculate the angles for. You can use multiple instances of this keyword i.e. ATOMS1, ATOMS2, ATOMS3...   

 ORIGIN  
calculate the distance of all the atoms specified using the ATOMS keyword from this point. For more information on how to specify lists of atoms see Groups and Virtual Atoms   

 LOCATION  
the location at which the CV is assumed to be in space. You can use multiple instances of this keyword i.e. LOCATION1, LOCATION2, LOCATION3...   

Options



 NOPBC  
( default=off ) ignore the periodic boundary conditions when calculating distances   

 COMPONENTS  
( default=off ) calculate the x, y and z components of the distance separately and store them as label.x, label.y and label.z   

 SCALED_COMPONENTS  
( default=off ) calculate the a, b and c scaled components of the distance separately and store them as label.a, label.b and label.c   

 LOWMEM  
( default=off ) this flag does nothing and is present only to ensure back-compatibility   

 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.   







  


    
   
    
     1.13.2