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.

Description of components

By default this Action calculates the following quantities. These quanties 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.	one or multiple instances of this quantity will be refereceable 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.
bias	total bias

Compulsory keywords

ARG

the input for this action is the output from one or more other actions. The particular output that you used is referenced using that action of interests label. If the label appears on its own then the value of the relevant Action is taken. If * or *.* appears the information from all arguments is taken. Some actions have multi-component outputs, each component of the output has a specific label so for instance an action labelled dist may have three componets 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.*

Options

NUMERICAL_DERIVATIVES

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

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

DISTANCE ATOMS=3,5 LABEL=d1
DISTANCE ATOMS=3,6 LABEL=d2
BIASVALUE ARG=d1,d2 LABEL=b
PRINT ARG=d1,d2,b.d1,b.d2

(See also DISTANCE and PRINT).

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

t: TIME
# this just print cos and sin of time
cos: MATHEVAL ARG=t VAR=t FUNC=cos(t) PERIODIC=NO
sin: MATHEVAL ARG=t VAR=t FUNC=sin(t) PERIODIC=NO
c1: COM ATOMS=1,2
c2: COM ATOMS=3,4
d: DISTANCE COMPONENTS ATOMS=c1,c2
PRINT ARG=t,cos,sin,d.x,d.y,d.z STRIDE=1 FILE=colvar FMT=%8.4f
# this calculates sine and cosine of a projected component of distance
mycos:  MATHEVAL ARG=d.x,d.y  VAR=x,y   FUNC=x/sqrt(x*x+y*y) PERIODIC=NO
mysin:  MATHEVAL ARG=d.x,d.y  VAR=x,y   FUNC=y/sqrt(x*x+y*y) PERIODIC=NO
# 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=mycos,mysin,cos,sin VAR=mc,ms,c,s  FUNC=100*((mc-c)^2+(ms-s)^2) PERIODIC=NO
# this takes the value calculated with matheval and uses as a bias
cc: BIASVALUE ARG=vv1
# some printout
PRINT ARG=t,cos,sin,d.x,d.y,d.z,mycos,mysin,cc.bias.vv1 STRIDE=1 FILE=colvar FMT=%8.4f

(see also TIME, MATHEVAL, COM, DISTANCE, and PRINT).