Shortcut: DISTANCES

Module	multicolvar
Description	Usage
Calculate the distances between multiple piars of atoms
output value	type
the DISTANCES between the each pair of atoms that were specified	vector

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
x	vector	COMPONENTS	the x-components of the distance vectors
y	vector	COMPONENTS	the y-components of the distance vectors
z	vector	COMPONENTS	the z-components of the distance vectors

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
GROUP	atoms	Calculate the distance between each distinct pair of atoms in the group
GROUPA	atoms	Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
GROUPB	atoms	Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
ATOMS	atoms	the pairs of atoms that you would like to calculate the angles for
ORIGIN	atoms	calculate the distance of all the atoms specified using the ATOMS keyword from this point
LOCATION	atoms	the location at which the CV is assumed to be in space

Further details and examples

Calculate the distances between multiple piars of atoms

This shortcut action allows you to calculate function of the distribution of distatnces 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 input tells plumed to calculate the distances between atoms 3 and 5 and between atoms 1 and 2 and to print the minimum for these two distances.

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

d1The DISTANCES action with label d1 calculates the following quantities: Quantity    Type    Description  
d1 vector the DISTANCES between the each pair of atoms that were specified
d1_min scalar the minimum colvar: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details 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}
# PLUMED interprets the command:
# d1: DISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1}
# as follows (Click the red comment above to revert to the short version of the input):
d1_vatom1The CENTER_FAST action with label d1_vatom1 calculates the following quantities: Quantity    Type    Description  
d1_vatom1 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=3,5
d1_vatom2The CENTER_FAST action with label d1_vatom2 calculates the following quantities: Quantity    Type    Description  
d1_vatom2 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=1,2
d1_grpThe GROUP action with label d1_grp calculates the following quantities: Quantity    Type    Description  
d1_grp atoms indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=d1_vatom1,d1_vatom2
d1The DISTANCE action with label d1 calculates the following quantities: Quantity    Type    Description  
d1 vector the DISTANCE for each set of specified atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=3,5 ATOMS2the pair of atom that we are calculating the distance between=1,2
d1_me_minThe CUSTOM action with label d1_me_min calculates the following quantities: Quantity    Type    Description  
d1_me_min vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d1 FUNCthe function you wish to evaluate=exp(0.1/x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d1_mec_minThe SUM action with label d1_mec_min calculates the following quantities: Quantity    Type    Description  
d1_mec_min scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=d1_me_min PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d1_minThe CUSTOM action with label d1_min calculates the following quantities: Quantity    Type    Description  
d1_min scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d1_mec_min FUNCthe function you wish to evaluate=0.1/log(x) 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=d1.min

The following input tells plumed to calculate the distances between atoms 3 and 5 and between atoms 1 and 2 and then to calculate the number of these distances that are less than 0.1 nm. The number of distances 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

d1The DISTANCES action with label d1 calculates the following quantities: Quantity    Type    Description  
d1 vector the DISTANCES between the each pair of atoms that were specified
d1_lessthan scalar the number of colvars that have a value less than a threshold: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details 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. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.1}
# PLUMED interprets the command:
# d1: DISTANCES ATOMS1=3,5 ATOMS2=1,2 LESS_THAN={RATIONAL R_0=0.1}
# as follows (Click the red comment above to revert to the short version of the input):
d1_vatom1The CENTER_FAST action with label d1_vatom1 calculates the following quantities: Quantity    Type    Description  
d1_vatom1 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=3,5
d1_vatom2The CENTER_FAST action with label d1_vatom2 calculates the following quantities: Quantity    Type    Description  
d1_vatom2 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=1,2
d1_grpThe GROUP action with label d1_grp calculates the following quantities: Quantity    Type    Description  
d1_grp atoms indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=d1_vatom1,d1_vatom2
d1The DISTANCE action with label d1 calculates the following quantities: Quantity    Type    Description  
d1 vector the DISTANCE for each set of specified atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=3,5 ATOMS2the pair of atom that we are calculating the distance between=1,2
d1_ltThe LESS_THAN action with label d1_lt calculates the following quantities: Quantity    Type    Description  
d1_lt vector the vector obtained by doing an element-wise application of a function that is one if the input is less than a threshold to the input vectors: LESS_THANUse a switching function to determine how many of the input variables are less than a certain cutoff. More details ARGthe values input to this function=d1 SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=0.1}
d1_lessthanThe SUM action with label d1_lessthan calculates the following quantities: Quantity    Type    Description  
d1_lessthan scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=d1_lt 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=d1.lessthan

The following input tells plumed to calculate all the distances between atoms 1, 2 and 3 (i.e. the distances between atoms 1 and 2, atoms 1 and 3 and atoms 2 and 3). The average of these distances is then calculated.

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

d1The DISTANCES action with label d1 calculates the following quantities: Quantity    Type    Description  
d1 vector the DISTANCES between the each pair of atoms that were specified
d1_mean scalar the mean of the colvars: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPCalculate the distance between each distinct pair of atoms in the group=1-3 MEAN calculate the mean of all the quantities
# PLUMED interprets the command:
# d1: DISTANCES GROUP=1-3 MEAN
# as follows (Click the red comment above to revert to the short version of the input):
d1The DISTANCE action with label d1 calculates the following quantities: Quantity    Type    Description  
d1 vector the DISTANCE for each set of specified atoms: DISTANCECalculate the distance/s between pairs of atoms. More details 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
d1_meanThe MEAN action with label d1_mean calculates the following quantities: Quantity    Type    Description  
d1_mean scalar the mean of all the elements in the input vector: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=d1 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=d1.mean

The following input tells plumed to calculate all the distances between the atoms in GROUPA and the atoms in GROUPB. In other words the distances between atoms 1 and 2 and the distance between atoms 1 and 3. The number of distances 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

d1The DISTANCES action with label d1 calculates the following quantities: Quantity    Type    Description  
d1 vector the DISTANCES between the each pair of atoms that were specified
d1_morethan scalar the number of colvars that have a value more than a threshold: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details 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. Options for this keyword are explained in the documentation for MORE_THAN.={RATIONAL R_0=0.1}
# PLUMED interprets the command:
# d1: DISTANCES GROUPA=1 GROUPB=2,3 MORE_THAN={RATIONAL R_0=0.1}
# as follows (Click the red comment above to revert to the short version of the input):
d1The DISTANCE action with label d1 calculates the following quantities: Quantity    Type    Description  
d1 vector the DISTANCE for each set of specified atoms: DISTANCECalculate the distance/s between pairs of atoms. More details 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
d1_mtThe MORE_THAN action with label d1_mt calculates the following quantities: Quantity    Type    Description  
d1_mt vector the vector obtained by doing an element-wise application of a function that is one if the if the input is more than a threshold to the input vectors: MORE_THANUse a switching function to determine how many of the input variables are more than a certain cutoff. More details ARGthe values input to this function=d1 SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=0.1}
d1_morethanThe SUM action with label d1_morethan calculates the following quantities: Quantity    Type    Description  
d1_morethan scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=d1_mt 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=d1.morethan

Calculating minimum distances

To calculate and print the minimum distance between two groups of atoms you use the following commands

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

d1The DISTANCES action with label d1 calculates the following quantities: Quantity    Type    Description  
d1 vector the DISTANCES between the each pair of atoms that were specified
d1_min scalar the minimum colvar: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=1-10 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=11-20 MINcalculate the minimum value={BETA=500.}
# PLUMED interprets the command:
# d1: DISTANCES GROUPA=1-10 GROUPB=11-20 MIN={BETA=500.}
# as follows (Click the red comment above to revert to the short version of the input):
d1The DISTANCE action with label d1 calculates the following quantities: Quantity    Type    Description  
d1 vector the DISTANCE for each set of specified atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=1,11 ATOMS2the pair of atom that we are calculating the distance between=1,12 ATOMS3the pair of atom that we are calculating the distance between=1,13 ATOMS4the pair of atom that we are calculating the distance between=1,14 ATOMS5the pair of atom that we are calculating the distance between=1,15     # Action input conctinues with 95 further ATOMSn keywords, 
d1_me_minThe CUSTOM action with label d1_me_min calculates the following quantities: Quantity    Type    Description  
d1_me_min vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d1 FUNCthe function you wish to evaluate=exp(500./x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d1_mec_minThe SUM action with label d1_mec_min calculates the following quantities: Quantity    Type    Description  
d1_mec_min scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=d1_me_min PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d1_minThe CUSTOM action with label d1_min calculates the following quantities: Quantity    Type    Description  
d1_min scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d1_mec_min FUNCthe function you wish to evaluate=500./log(x) 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=d1.min 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

In order to ensure that the minimum value has continuous derivatives we use the following function:

$s = \frac{\beta}{ \log \sum_i \exp\left( \frac{\beta}{s_i} \right) }$

where $\beta$ is a user specified parameter.

This input is used rather than a separate MINDIST colvar so that the same routine and the same input style can be used to calculate minimum coordination numbers (see COORDINATIONNUMBER), minimum angles (see ANGLES) and many other variables.

This new way of calculating mindist is part of plumed 2's multicolvar functionality. These special actions allow you to calculate multiple functions of a distribution of simple collective variables. As an example you can calculate the number of distances less than 1.0, the minimum distance, the number of distances more than 2.0 and the number of distances between 1.0 and 2.0 by using the following command:

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

d1The DISTANCES action with label d1 calculates the following quantities: Quantity    Type    Description  
d1 vector the DISTANCES between the each pair of atoms that were specified
d1_lessthan scalar the number of colvars that have a value less than a threshold
d1_morethan scalar the number of colvars that have a value more than a threshold
d1_min scalar the minimum colvar
d1_between scalar the number of colvars that have a value that lies in a particular interval: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details ...
 GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=1-10 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=11-20
 LESS_THANcalculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.0}
 MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={RATIONAL R_0=2.0}
 BETWEENcalculate the number of values that are within a certain range. Options for this keyword are explained in the documentation for BETWEEN.={GAUSSIAN LOWER=1.0 UPPER=2.0}
 MINcalculate the minimum value={BETA=500.}
...
# PLUMED interprets the command:
# d1: DISTANCES ...
#  GROUPA=1-10 GROUPB=11-20
#  LESS_THAN={RATIONAL R_0=1.0}
#  MORE_THAN={RATIONAL R_0=2.0}
#  BETWEEN={GAUSSIAN LOWER=1.0 UPPER=2.0}
#  MIN={BETA=500.}
# ...
# as follows (Click the red comment above to revert to the short version of the input):
d1The DISTANCE action with label d1 calculates the following quantities: Quantity    Type    Description  
d1 vector the DISTANCE for each set of specified atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=1,11 ATOMS2the pair of atom that we are calculating the distance between=1,12 ATOMS3the pair of atom that we are calculating the distance between=1,13 ATOMS4the pair of atom that we are calculating the distance between=1,14 ATOMS5the pair of atom that we are calculating the distance between=1,15     # Action input conctinues with 95 further ATOMSn keywords, 
d1_ltThe LESS_THAN action with label d1_lt calculates the following quantities: Quantity    Type    Description  
d1_lt vector the vector obtained by doing an element-wise application of a function that is one if the input is less than a threshold to the input vectors: LESS_THANUse a switching function to determine how many of the input variables are less than a certain cutoff. More details ARGthe values input to this function=d1 SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=1.0}
d1_lessthanThe SUM action with label d1_lessthan calculates the following quantities: Quantity    Type    Description  
d1_lessthan scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=d1_lt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d1_mtThe MORE_THAN action with label d1_mt calculates the following quantities: Quantity    Type    Description  
d1_mt vector the vector obtained by doing an element-wise application of a function that is one if the if the input is more than a threshold to the input vectors: MORE_THANUse a switching function to determine how many of the input variables are more than a certain cutoff. More details ARGthe values input to this function=d1 SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=2.0}
d1_morethanThe SUM action with label d1_morethan calculates the following quantities: Quantity    Type    Description  
d1_morethan scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=d1_mt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d1_me_minThe CUSTOM action with label d1_me_min calculates the following quantities: Quantity    Type    Description  
d1_me_min vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d1 FUNCthe function you wish to evaluate=exp(500./x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d1_mec_minThe SUM action with label d1_mec_min calculates the following quantities: Quantity    Type    Description  
d1_mec_min scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=d1_me_min PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d1_minThe CUSTOM action with label d1_min calculates the following quantities: Quantity    Type    Description  
d1_min scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d1_mec_min FUNCthe function you wish to evaluate=500./log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d1_btThe BETWEEN action with label d1_bt calculates the following quantities: Quantity    Type    Description  
d1_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=d1 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=1.0 UPPER=2.0}
d1_betweenThe SUM action with label d1_between calculates the following quantities: Quantity    Type    Description  
d1_between scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=d1_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=d1.lessthan,d1.morethan,d1.between,d1.min 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

A calculation performed this way is fast because the expensive part of the calculation - the calculation of all the distances - is only done once per step.

Syntax

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

Keyword	Type	Default	Description
GROUP	input	none	Calculate the distance between each distinct pair of atoms in the group
GROUPA	input	none	Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
GROUPB	input	none	Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
ATOMS	input	none	the pairs of atoms that you would like to calculate the angles for
ORIGIN	input	none	calculate the distance of all the atoms specified using the ATOMS keyword from this point
LOCATION	input	none	the location at which the CV is assumed to be in space
NOPBC	optional	false	ignore the periodic boundary conditions when calculating distances
COMPONENTS	optional	false	calculate the x, y and z components of the distance separately and store them as label
SCALED_COMPONENTS	optional	false	calculate the a, b and c scaled components of the distance separately and store them as label
LOWMEM	optional	false	this flag does nothing and is present only to ensure back-compatibility
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	false	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	false	this flag allows you to recover the lowest of these variables
SUM	optional	false	calculate the sum of all the quantities
MEAN	optional	false	calculate the mean of all the quantities

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Quantity	Type	Description
d1	vector	the DISTANCES between the each pair of atoms that were specified
d1_min	scalar	the minimum colvar