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| 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.
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 | the instantaneous value of the bias potential |
| _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. |
| 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 proceding 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 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.*.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... |
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
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
1.8.14