BIASVALUE

This is part of the bias module

Takes the value of one variable and use it as a bias

This is the simplest possible bias: the bias potential is equal to a collective variable. It is useful to create custom biasing potential, e.g. applying a function (see Functions) to some collective variable then using the value of this function directly as a bias.

Examples

The following input tells plumed to use the value of the distance between atoms 3 and 5 and the value of the distance between atoms 2 and 4 as biases. It then tells plumed to print the energy of the restraint

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

d1: DISTANCE 
ATOMS
the pair of atom that we are calculating the distance between. 
=3,5 The DISTANCE action with label d1 calculates a single scalar value
d2: DISTANCE 
ATOMS
the pair of atom that we are calculating the distance between. 
=3,6 The DISTANCE action with label d2 calculates a single scalar value
b: BIASVALUE 
ARG
the input for this action is the scalar output from one or more other actions. 
=d1,d2 The BIASVALUE action with label b calculates the following quantities:

 Quantity   
 Description  
b.bias
the instantaneous value of the bias potential
b.d1_bias
one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with  the arguments of the bias followed by the character string _bias. These quantities tell the user how much the bias is due to each of the colvars. This particular component measures this quantity for the input CV named d1
b.d2_bias
one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with  the arguments of the bias followed by the character string _bias. These quantities tell the user how much the bias is due to each of the colvars. This particular component measures this quantity for the input CV named d2


PRINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=d1,d2,b.d1_bias,b.d2_bias The PRINT action with label 

Another thing one can do is asking one system to follow a circle in sin/cos according a time dependence

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

contract shortcuts

t: TIME The TIME action with label t calculates a single scalar value
# this just print cos and sin of time
cos: MATHEVAL 
ARG
the input to this function. 
=t 
VAR
the names to give each of the arguments in the function. 
=t 
FUNC
compulsory keyword 
the function you wish to evaluate 
=cos(t) 
PERIODIC
compulsory keyword 
if the output of your function is periodic then you should specify the periodicity
of the function. 
=NO The MATHEVAL action with label cos calculates a single scalar value
sin: MATHEVAL 
ARG
the input to this function. 
=t 
VAR
the names to give each of the arguments in the function. 
=t 
FUNC
compulsory keyword 
the function you wish to evaluate 
=sin(t) 
PERIODIC
compulsory keyword 
if the output of your function is periodic then you should specify the periodicity
of the function. 
=NO The MATHEVAL action with label sin calculates a single scalar value
c1: COM 
ATOMS
the list of atoms which are involved the virtual atom's definition. 
=1,2 The COM action with label c1 calculates the following quantities:

 Quantity   
 Description  
c1.x
the x coordinate of the virtual atom
c1.y
the y coordinate of the virtual atom
c1.z
the z coordinate of the virtual atom
c1.mass
the mass of the virtual atom
c1.charge
the charge of the virtual atom


c2: COM 
ATOMS
the list of atoms which are involved the virtual atom's definition. 
=3,4 The COM action with label c2 calculates the following quantities:

 Quantity   
 Description  
c2.x
the x coordinate of the virtual atom
c2.y
the y coordinate of the virtual atom
c2.z
the z coordinate of the virtual atom
c2.mass
the mass of the virtual atom
c2.charge
the charge of the virtual atom


d: DISTANCE 
COMPONENTS
( default=off ) calculate the x, y and z components of the distance separately and
store them as label.x, 
 
ATOMS
the pair of atom that we are calculating the distance between. 
=c1,c2 The DISTANCE action with label d calculates the following quantities:

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


PRINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=t,cos,sin,d.x,d.y,d.z 
STRIDE
compulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output 
=1 
FILE
the name of the file on which to output these quantities 
=colvar 
FMT
the format that should be used to output real numbers 
=%8.4f The PRINT action with label 
# this calculates sine and cosine of a projected component of distance
mycos: MATHEVAL 
ARG
the input to this function. 
=d.x,d.y 
VAR
the names to give each of the arguments in the function. 
=x,y 
FUNC
compulsory keyword 
the function you wish to evaluate 
=x/sqrt(x*x+y*y) 
PERIODIC
compulsory keyword 
if the output of your function is periodic then you should specify the periodicity
of the function. 
=NO The MATHEVAL action with label mycos calculates a single scalar value
mysin: MATHEVAL 
ARG
the input to this function. 
=d.x,d.y 
VAR
the names to give each of the arguments in the function. 
=x,y 
FUNC
compulsory keyword 
the function you wish to evaluate 
=y/sqrt(x*x+y*y) 
PERIODIC
compulsory keyword 
if the output of your function is periodic then you should specify the periodicity
of the function. 
=NO The MATHEVAL action with label mysin calculates a single scalar value
# this creates a moving spring so that the system follows a circle-like dynamics
# but it is not a bias, it is a simple value now
vv1: MATHEVAL 
ARG
the input to this function. 
=mycos,mysin,cos,sin 
VAR
the names to give each of the arguments in the function. 
=mc,ms,c,s 
FUNC
compulsory keyword 
the function you wish to evaluate 
=100*((mc-c)^2+(ms-s)^2) 
PERIODIC
compulsory keyword 
if the output of your function is periodic then you should specify the periodicity
of the function. 
=NO The MATHEVAL action with label vv1 calculates a single scalar value
# this takes the value calculated with matheval and uses as a bias
cc: BIASVALUE 
ARG
the input for this action is the scalar output from one or more other actions. 
=vv1 The BIASVALUE action with label cc calculates the following quantities:

 Quantity   
 Description  
cc.bias
the instantaneous value of the bias potential
cc.vv1_bias
one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with  the arguments of the bias followed by the character string _bias. These quantities tell the user how much the bias is due to each of the colvars. This particular component measures this quantity for the input CV named vv1


# some printout
PRINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=t,cos,sin,d.x,d.y,d.z,mycos,mysin,cc.vv1_bias 
STRIDE
compulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output 
=1 
FILE
the name of the file on which to output these quantities 
=colvar 
FMT
the format that should be used to output real numbers 
=%8.4f The PRINT action with label 

t: TIME The TIME action with label t calculates a single scalar value
# this just print cos and sin of time
cos: MATHEVAL_SCALAR 
ARG
the input for this action is the scalar output from one or more other actions. 
=t 
VAR
the names to give each of the arguments in the function. 
=t 
FUNC
compulsory keyword 
the function you wish to evaluate 
=cos(t) 
PERIODIC
compulsory keyword 
if the output of your function is periodic then you should specify the periodicity
of the function. 
=NO The MATHEVAL_SCALAR action with label cos calculates a single scalar value
sin: MATHEVAL_SCALAR 
ARG
the input for this action is the scalar output from one or more other actions. 
=t 
VAR
the names to give each of the arguments in the function. 
=t 
FUNC
compulsory keyword 
the function you wish to evaluate 
=sin(t) 
PERIODIC
compulsory keyword 
if the output of your function is periodic then you should specify the periodicity
of the function. 
=NO The MATHEVAL_SCALAR action with label sin calculates a single scalar value
c1: COM 
ATOMS
the list of atoms which are involved the virtual atom's definition. 
=1,2 The COM action with label c1 calculates the following quantities:

 Quantity   
 Description  
c1.x
the x coordinate of the virtual atom
c1.y
the y coordinate of the virtual atom
c1.z
the z coordinate of the virtual atom
c1.mass
the mass of the virtual atom
c1.charge
the charge of the virtual atom


c2: COM 
ATOMS
the list of atoms which are involved the virtual atom's definition. 
=3,4 The COM action with label c2 calculates the following quantities:

 Quantity   
 Description  
c2.x
the x coordinate of the virtual atom
c2.y
the y coordinate of the virtual atom
c2.z
the z coordinate of the virtual atom
c2.mass
the mass of the virtual atom
c2.charge
the charge of the virtual atom


d: DISTANCE 
COMPONENTS
( default=off ) calculate the x, y and z components of the distance separately and
store them as label.x, 
 
ATOMS
the pair of atom that we are calculating the distance between. 
=c1,c2 The DISTANCE action with label d calculates the following quantities:

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


PRINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=t,cos,sin,d.x,d.y,d.z 
STRIDE
compulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output 
=1 
FILE
the name of the file on which to output these quantities 
=colvar 
FMT
the format that should be used to output real numbers 
=%8.4f The PRINT action with label 
# this calculates sine and cosine of a projected component of distance
mycos: MATHEVAL_SCALAR 
ARG
the input for this action is the scalar output from one or more other actions. 
=d.x,d.y 
VAR
the names to give each of the arguments in the function. 
=x,y 
FUNC
compulsory keyword 
the function you wish to evaluate 
=x/sqrt(x*x+y*y) 
PERIODIC
compulsory keyword 
if the output of your function is periodic then you should specify the periodicity
of the function. 
=NO The MATHEVAL_SCALAR action with label mycos calculates a single scalar value
mysin: MATHEVAL_SCALAR 
ARG
the input for this action is the scalar output from one or more other actions. 
=d.x,d.y 
VAR
the names to give each of the arguments in the function. 
=x,y 
FUNC
compulsory keyword 
the function you wish to evaluate 
=y/sqrt(x*x+y*y) 
PERIODIC
compulsory keyword 
if the output of your function is periodic then you should specify the periodicity
of the function. 
=NO The MATHEVAL_SCALAR action with label mysin calculates a single scalar value
# this creates a moving spring so that the system follows a circle-like dynamics
# but it is not a bias, it is a simple value now
vv1: MATHEVAL_SCALAR 
ARG
the input for this action is the scalar output from one or more other actions. 
=mycos,mysin,cos,sin 
VAR
the names to give each of the arguments in the function. 
=mc,ms,c,s 
FUNC
compulsory keyword 
the function you wish to evaluate 
=100*((mc-c)^2+(ms-s)^2) 
PERIODIC
compulsory keyword 
if the output of your function is periodic then you should specify the periodicity
of the function. 
=NO The MATHEVAL_SCALAR action with label vv1 calculates a single scalar value
# this takes the value calculated with matheval and uses as a bias
cc: BIASVALUE 
ARG
the input for this action is the scalar output from one or more other actions. 
=vv1 The BIASVALUE action with label cc calculates the following quantities:

 Quantity   
 Description  
cc.bias
the instantaneous value of the bias potential
cc.vv1_bias
one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with  the arguments of the bias followed by the character string _bias. These quantities tell the user how much the bias is due to each of the colvars. This particular component measures this quantity for the input CV named vv1


# some printout
PRINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=t,cos,sin,d.x,d.y,d.z,mycos,mysin,cc.vv1_bias 
STRIDE
compulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output 
=1 
FILE
the name of the file on which to output these quantities 
=colvar 
FMT
the format that should be used to output real numbers 
=%8.4f The PRINT action with label 

Glossary of keywords and components

Description of components

By default this Action calculates the following quantities. These quantities can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the quantity required from the list below.

Quantity	Description
bias	the instantaneous value of the bias potential
_bias	one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with the arguments of the bias followed by the character string _bias. These quantities tell the user how much the bias is due to each of the colvars.

Options

NUMERICAL_DERIVATIVES

( default=off ) calculate the derivatives for these quantities numerically

ARG

the input for this action is the scalar output from one or more other actions. The particular scalars that you will use are referenced using the label of the action. If the label appears on its own then it is assumed that the Action calculates a single scalar value. The value of this scalar is thus used as the input to this new action. If * or *.* appears the scalars calculated by all the proceeding actions in the input file are taken. Some actions have multi-component outputs and each component of the output has a specific label. For example a DISTANCE action labelled dist may have three components x, y and z. To take just the x component you should use dist.x, if you wish to take all three components then use dist.*.More information on the referencing of Actions can be found in the section of the manual on the PLUMED Getting Started. Scalar values can also be referenced using POSIX regular expressions as detailed in the section on Regular Expressions. To use this feature you you must compile PLUMED with the appropriate flag.. You can use multiple instances of this keyword i.e. ARG1, ARG2, ARG3...