RESCALE
This is part of the isdb module

Rescales the value of an another action, being a Collective Variable or a Bias.

The rescaling factor is determined by a parameter defined on a logarithmic grid of dimension NBIN in the range from 1 to MAX_RESCALE. The current value of the rescaling parameter is stored and shared across other actions using a SELECTOR. A Monte Carlo procedure is used to update the value of the rescaling factor every MC_STRIDE steps of molecular dynamics. Well-tempered metadynamics, defined by the parameters W0 and BIASFACTOR, is used to enhance the sampling in the space of the rescaling factor. The well-tempered metadynamics bias potential is written to the file BFILE every BSTRIDE steps and read when restarting the simulation using the directive RESTART.

Note
Additional arguments not to be rescaled, one for each bin in the rescaling parameter ladder, can be provided at the end of the ARG list. The number of such arguments is specified by the option NOT_RESCALED. These arguments will be not be rescaled, but they will be considered as bias potentials and used in the computation of the Metropolis acceptance probability when proposing a move in the rescaling parameter. See example below.
If PLUMED is running in a multiple-replica framework (for example using the -multi option in GROMACS), the arguments will be summed across replicas, unless the NOT_SHARED option is used. Also, the value of the SELECTOR will be shared and thus will be the same in all replicas.
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 the instantaneous value of the bias potential
igamma gamma parameter
accgamma MC acceptance for gamma
wtbias well-tempered bias
Compulsory keywords
TEMP temperature
SELECTOR name of the SELECTOR used for rescaling
MAX_RESCALE maximum values for rescaling
NBIN number of bins for gamma grid
W0 initial bias height
BIASFACTOR bias factor
BSTRIDE stride for writing bias
BFILE file name for bias
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 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...
NOT_SHARED list of arguments (from 1 to N) not summed across replicas
NOT_RESCALED these last N arguments will not be rescaled
MC_STEPS number of MC steps
MC_STRIDE MC stride
PACE

Pace for adding bias, in MC stride unit

Examples

In this example we use RESCALE to implement a simulated-tempering like approach. The total potential energy of the system is rescaled by a parameter defined on a logarithmic grid of 5 bins in the range from 1 to 1.5. A well-tempered metadynamics bias potential is used to ensure diffusion in the space of the rescaling parameter.

ene: ENERGY

SELECTOR NAME=GAMMA VALUE=0

RESCALE ...
LABEL=res ARG=ene TEMP=300
SELECTOR=GAMMA MAX_RESCALE=1.5 NBIN=5
W0=1000 BIASFACTOR=100.0 BSTRIDE=2000 BFILE=bias.dat
...

PRINT FILE=COLVAR ARG=* STRIDE=100

In this second example, we add to the simulated-tempering approach introduced above one Parallel Bias metadynamics simulation (see PBMETAD) for each value of the rescaling parameter. At each moment of the simulation, only one of the PBMETAD actions is activated, based on the current value of the associated SELECTOR. The PBMETAD bias potentials are not rescaled, but just used in the calculation of the Metropolis acceptance probability when proposing a move in the rescaling parameter.

ene: ENERGY
d: DISTANCE ATOMS=1,2

SELECTOR NAME=GAMMA VALUE=0

pbmetad0: PBMETAD ARG=d SELECTOR=GAMMA SELECTOR_ID=0 SIGMA=0.1 PACE=500 HEIGHT=1 BIASFACTOR=8 FILE=HILLS.0
pbmetad1: PBMETAD ARG=d SELECTOR=GAMMA SELECTOR_ID=1 SIGMA=0.1 PACE=500 HEIGHT=1 BIASFACTOR=8 FILE=HILLS.1
pbmetad2: PBMETAD ARG=d SELECTOR=GAMMA SELECTOR_ID=2 SIGMA=0.1 PACE=500 HEIGHT=1 BIASFACTOR=8 FILE=HILLS.2
pbmetad3: PBMETAD ARG=d SELECTOR=GAMMA SELECTOR_ID=3 SIGMA=0.1 PACE=500 HEIGHT=1 BIASFACTOR=8 FILE=HILLS.3
pbmetad4: PBMETAD ARG=d SELECTOR=GAMMA SELECTOR_ID=4 SIGMA=0.1 PACE=500 HEIGHT=1 BIASFACTOR=8 FILE=HILLS.4

RESCALE ...
LABEL=res TEMP=300
ARG=ene,pbmetad0.bias,pbmetad1.bias,pbmetad2.bias,pbmetad3.bias,pbmetad4.bias
SELECTOR=GAMMA MAX_RESCALE=1.5 NOT_RESCALED=5 NBIN=5
W0=1000 BIASFACTOR=100.0 BSTRIDE=2000 BFILE=bias.dat
...

PRINT FILE=COLVAR ARG=* STRIDE=100