Shortcut: INPLANEDISTANCES

Module	multicolvar
Description	Usage
Calculate distances in the plane perpendicular to an axis
output value	type
the INPLANEDISTANCE between each of the atoms specified using the GROUP keyword and atom A in the plane perpendicular to the vector connecting the atoms specified using VECTORSTART and VECTOREND	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

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 distance for each distinct set of three atoms in the group
VECTORSTART	atoms	The first atom position that is used to define the normal to the plane of interest
VECTOREND	atoms	The second atom position that is used to defin the normal to the plane of interest

Further details and examples

Calculate distances in the plane perpendicular to an axis

Each quantity calculated in this CV uses the positions of two atoms, this indices of which are specified using the VECTORSTART and VECTOREND keywords, to specify the orientation of a vector, $\mathbf{n}$ . The perpendicular distance between this vector and the position of some third atom is then computed using:

$x_j = |\mathbf{r}_{j}| \sin (\theta_j)$

where $\mathbf{r}_j$ is the distance between one of the two atoms that define the vector $\mathbf{n}$ and a third atom (atom $j$ ) and where $\theta_j$ is the angle between the vector \f $\mathbf{n}\f$ and the vector $\mathbf{r}_{j}$ . The $x_j$ values for each of the atoms specified using the GROUP keyword are calculated. Keywords such as MORE_THAN and LESS_THAN can then be used to calculate the number of these quantities that are more or less than a given cutoff.

The following input can be used to calculate the number of atoms that have indices greater than 3 and less than 101 that are within a cylinder with a radius of 0.3 nm that has its long axis aligned with the vector connecting atoms 1 and 2.

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

d1The INPLANEDISTANCES action with label d1 calculates the following quantities: Quantity    Type    Description  
d1 vector the INPLANEDISTANCE between each of the atoms specified using the GROUP keyword and atom A in the plane perpendicular to the vector connecting the atoms specified using VECTORSTART and VECTOREND
d1_lessthan scalar the number of colvars that have a value less than a threshold: INPLANEDISTANCESCalculate distances in the plane perpendicular to an axis This action is a shortcut. More details VECTORSTARTThe first atom position that is used to define the normal to the plane of interest=1 VECTORENDThe second atom position that is used to defin the normal to the plane of interest=2 GROUPcalculate distance for each distinct set of three atoms in the group=3-100 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 D_0=0.2 R_0=0.1}
# PLUMED interprets the command:
# d1: INPLANEDISTANCES VECTORSTART=1 VECTOREND=2 GROUP=3-100 LESS_THAN={RATIONAL D_0=0.2 R_0=0.1}
# as follows (Click the red comment above to revert to the short version of the input):
d1_disThe DISTANCE action with label d1_dis calculates the following quantities: Quantity    Type    Description  
d1_dis 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=1,3 ATOMS2the pair of atom that we are calculating the distance between=1,4 ATOMS3the pair of atom that we are calculating the distance between=1,5 ATOMS4the pair of atom that we are calculating the distance between=1,6 ATOMS5the pair of atom that we are calculating the distance between=1,7     # Action input conctinues with 93 further ATOMSn keywords, 
d1_angThe ANGLE action with label d1_ang calculates the following quantities: Quantity    Type    Description  
d1_ang vector the ANGLE for each set of specified atoms: ANGLECalculate one or multiple angle/s. More details ATOMS1the list of atoms involved in this collective variable (either 3 or 4 atoms)=2,1,3 ATOMS2the list of atoms involved in this collective variable (either 3 or 4 atoms)=2,1,4 ATOMS3the list of atoms involved in this collective variable (either 3 or 4 atoms)=2,1,5 ATOMS4the list of atoms involved in this collective variable (either 3 or 4 atoms)=2,1,6 ATOMS5the list of atoms involved in this collective variable (either 3 or 4 atoms)=2,1,7     # Action input conctinues with 93 further ATOMSn keywords, 
d1The CUSTOM action with label d1 calculates the following quantities: Quantity    Type    Description  
d1 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 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe function you wish to evaluate=x*sin(y) ARGthe values input to this function=d1_dis,d1_ang
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 D_0=0.2 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 FILEthe name of the file on which to output these quantities=colvar

Notice that the INPLANEDISTANCES is a shortcut. The syntax that is described in the expanded version of the input above provides much more flexibility for designing new CVs.

Syntax

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

Keyword	Type	Default	Description
GROUP	input	none	calculate distance for each distinct set of three atoms in the group
VECTORSTART	input	none	The first atom position that is used to define the normal to the plane of interest
VECTOREND	input	none	The second atom position that is used to defin the normal to the plane of interest
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 INPLANEDISTANCE between each of the atoms specified using the GROUP keyword and atom A in the plane perpendicular to the vector connecting the atoms specified using VECTORSTART and VECTOREND
d1_lessthan	scalar	the number of colvars that have a value less than a threshold