Action: BIASVALUE

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

Output components

This action calculates the values in the following table. 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.

Input

The arguments that serve as the input for this action are specified using one or more of the keywords in the following table.

Further details and examples

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

This is the simplest possible bias: when you use this method the bias potential is set equal to the scalar-valued argument that was input. This action is useful for creating custom biasing potential, e.g. if you apply a function (see function module) to some collective variable then use the value of this function directly as a bias.

This action is also useful for testing that forces are being calculated correctly. If I wanted to test whether the derivatives calculated by the DISTANCE action are computed correctly I would write a PLUMED input like this one:

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

d1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2
BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=d1

I would then run a calculation using driver with the following input:

plumed driveranalyze trajectories with plumed This action has hidden defaults. More details --ixyzthe trajectory in xyz format traj.xyz --debug-forcesoutput a file containing the forces due to the bias evaluated using numerical derivatives and using the analytical derivatives implemented in plumed forces.num

The driver action with label plumed calculates somethingplumed driveranalyze trajectories with plumed This action uses the defaults shown here. More details --ixyzthe trajectory in xyz format traj.xyz --debug-forcesoutput a file containing the forces due to the bias evaluated using numerical derivatives and using the analytical derivatives implemented in plumed forces.num
 --plumed specify the name of the plumed input file plumed.dat --timestep the timestep that was used in the calculation that produced this trajectory in picoseconds 1.0 --trajectory-stride the frequency with which frames were output to this trajectory during the simulation (0 means that the number of the step is read from the trajectory file, currently working only for xtc/trr files read with --ixtc/--trr) 1 --multi set number of replicas for multi environment (needs MPI) 0 --dump-forces-fmt the format to use to dump the forces %%f 

This outputs a file with two columns that both contain the forces that are acting upon the atoms. The first set of forces output are the analytic forces that are implemented within PLUMED. The second set of forces are calcluated numerically using finite difference. If you method is implemented correctly these two sets of forces should be the same.

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

DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3,5 LABELa label for the action so that its output can be referenced in the input to other actions=d1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1
scalar
the DISTANCE between this pair of atoms
DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3,6 LABELa label for the action so that its output can be referenced in the input to other actions=d2The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Type   
 Description  
d2
scalar
the DISTANCE between this pair of atoms
BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=d1,d2 LABELa label for the action so that its output can be referenced in the input to other actions=bThe BIASVALUE action with label b calculates the following quantities:
 Quantity   
 Type   
 Description  
b.bias
scalar
the instantaneous value of the bias potential
b.d1_bias
scalar
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
scalar
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
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d1,d2,b.d1_bias,b.d2_bias

Another thing one can do is ask the system to follow a circle in sin/cos in accordance with a time dependence

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

tThe TIME action with label t calculates the following quantities:
 Quantity   
 Type   
 Description  
t
scalar
the time since the start of the trajectory: TIMEretrieve the time of the simulation to be used elsewhere More details
# this just print cos and sin of time
cosThe MATHEVAL action with label cos calculates the following quantities:
 Quantity   
 Type   
 Description  
cos
scalar
an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t VARthe names to give each of the arguments in the function=t FUNCthe function you wish to evaluate=cos(t) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
sinThe MATHEVAL action with label sin calculates the following quantities:
 Quantity   
 Type   
 Description  
sin
scalar
an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t VARthe names to give each of the arguments in the function=t FUNCthe function you wish to evaluate=sin(t) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
c1The COM action with label c1 calculates the following quantities:
 Quantity   
 Type   
 Description  
c1
atoms
virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1,2
c2The COM action with label c2 calculates the following quantities:
 Quantity   
 Type   
 Description  
c2
atoms
virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3,4
dThe DISTANCE action with label d calculates the following quantities:
 Quantity   
 Type   
 Description  
d.x
scalar
the x-component of the vector connecting the two atoms
d.y
scalar
the y-component of the vector connecting the two atoms
d.z
scalar
the z-component of the vector connecting the two atoms: DISTANCECalculate the distance/s between pairs of atoms. More details COMPONENTS calculate the x, y and z components of the distance separately and store them as label ATOMSthe pair of atom that we are calculating the distance between=c1,c2
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=t,cos,sin,d.x,d.y,d.z STRIDE the frequency with which the quantities of interest should be output=1 FILEthe name of the file on which to output these quantities=colvar FMTthe format that should be used to output real numbers=%8.4f
# this calculates sine and cosine of a projected component of distance
The PRINT action with label  calculates somethingmycosThe MATHEVAL action with label mycos calculates the following quantities:
 Quantity   
 Type   
 Description  
mycos
scalar
an arbitrary function:  MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=d.x,d.y  VARthe names to give each of the arguments in the function=x,y   FUNCthe function you wish to evaluate=x/sqrt(x*x+y*y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
mysinThe MATHEVAL action with label mysin calculates the following quantities:
 Quantity   
 Type   
 Description  
mysin
scalar
an arbitrary function:  MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=d.x,d.y  VARthe names to give each of the arguments in the function=x,y   FUNCthe function you wish to evaluate=y/sqrt(x*x+y*y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=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
vv1The MATHEVAL action with label vv1 calculates the following quantities:
 Quantity   
 Type   
 Description  
vv1
scalar
an arbitrary function:  MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=mycos,mysin,cos,sin VARthe names to give each of the arguments in the function=mc,ms,c,s  FUNCthe function you wish to evaluate=100*((mc-c)^2+(ms-s)^2) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# this takes the value calculated with matheval and uses as a bias
ccThe BIASVALUE action with label cc calculates the following quantities:
 Quantity   
 Type   
 Description  
cc.bias
scalar
the instantaneous value of the bias potential
cc.vv1_bias
scalar
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: BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=vv1
# some printout
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=t,cos,sin,d.x,d.y,d.z,mycos,mysin,cc.vv1_bias STRIDE the frequency with which the quantities of interest should be output=1 FILEthe name of the file on which to output these quantities=colvar FMTthe format that should be used to output real numbers=%8.4f

Syntax

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