RESCALE
 This is part of the isdb module

Scales 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 scaled, 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 scaled, 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.
Examples

In this example we use RESCALE to implement a simulated-tempering like approach. The total potential energy of the system is scaled 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.

Click on the labels of the actions for more information on what each action computes
ene: ENERGY
SELECTOR NAMEcompulsory keyword
name of the SELECTOR =GAMMA VALUEcompulsory keyword
set (initial) value of the SELECTOR =0
res: RESCALE ...
ARGthe input for this action is the scalar output from one or more other actions. =ene TEMPcompulsory keyword
temperature =300
SELECTORcompulsory keyword
name of the SELECTOR used for rescaling =GAMMA MAX_RESCALEcompulsory keyword
maximum values for rescaling =1.5 NBINcompulsory keyword
number of bins for gamma grid =5
W0 could not find this keyword =1000 BIASFACTORcompulsory keyword
bias factor =100.0 BSTRIDEcompulsory keyword
stride for writing bias =2000 BFILEcompulsory keyword
file name for bias =bias.dat
...
PRINT FILEthe name of the file on which to output these quantities =COLVAR ARGthe input for this action is the scalar output from one or more other actions. =* STRIDEcompulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output =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 scaled, but just used in the calculation of the Metropolis acceptance probability when proposing a move in the rescaling parameter.

Click on the labels of the actions for more information on what each action computes
ene: ENERGY
d: DISTANCE ATOMSthe pair of atom that we are calculating the distance between. =1,2
SELECTOR NAMEcompulsory keyword
name of the SELECTOR =GAMMA VALUEcompulsory keyword
set (initial) value of the SELECTOR =0
pbmetad0: PBMETAD ARGthe input for this action is the scalar output from one or more other actions. =d SELECTORadd forces and do update based on the value of SELECTOR =GAMMA SELECTOR_IDvalue of SELECTOR =0 SIGMAcompulsory keyword
the widths of the Gaussian hills =0.1 PACEcompulsory keyword
the frequency for hill addition, one for all biases =500 HEIGHTthe height of the Gaussian hills, one for all biases. =1 BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases. =8 FILEfiles in which the lists of added hills are stored, default names are assigned using
pbmetad1: PBMETAD ARGthe input for this action is the scalar output from one or more other actions. =d SELECTORadd forces and do update based on the value of SELECTOR =GAMMA SELECTOR_IDvalue of SELECTOR =1 SIGMAcompulsory keyword
the widths of the Gaussian hills =0.1 PACEcompulsory keyword
the frequency for hill addition, one for all biases =500 HEIGHTthe height of the Gaussian hills, one for all biases. =1 BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases. =8 FILEfiles in which the lists of added hills are stored, default names are assigned using
pbmetad2: PBMETAD ARGthe input for this action is the scalar output from one or more other actions. =d SELECTORadd forces and do update based on the value of SELECTOR =GAMMA SELECTOR_IDvalue of SELECTOR =2 SIGMAcompulsory keyword
the widths of the Gaussian hills =0.1 PACEcompulsory keyword
the frequency for hill addition, one for all biases =500 HEIGHTthe height of the Gaussian hills, one for all biases. =1 BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases. =8 FILEfiles in which the lists of added hills are stored, default names are assigned using
pbmetad3: PBMETAD ARGthe input for this action is the scalar output from one or more other actions. =d SELECTORadd forces and do update based on the value of SELECTOR =GAMMA SELECTOR_IDvalue of SELECTOR =3 SIGMAcompulsory keyword
the widths of the Gaussian hills =0.1 PACEcompulsory keyword
the frequency for hill addition, one for all biases =500 HEIGHTthe height of the Gaussian hills, one for all biases. =1 BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases. =8 FILEfiles in which the lists of added hills are stored, default names are assigned using
pbmetad4: PBMETAD ARGthe input for this action is the scalar output from one or more other actions. =d SELECTORadd forces and do update based on the value of SELECTOR =GAMMA SELECTOR_IDvalue of SELECTOR =4 SIGMAcompulsory keyword
the widths of the Gaussian hills =0.1 PACEcompulsory keyword
the frequency for hill addition, one for all biases =500 HEIGHTthe height of the Gaussian hills, one for all biases. =1 BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases. =8 FILEfiles in which the lists of added hills are stored, default names are assigned using
res: RESCALE ...
TEMPcompulsory keyword
temperature =300
SELECTORcompulsory keyword
name of the SELECTOR used for rescaling =GAMMA MAX_RESCALEcompulsory keyword
maximum values for rescaling =1.5 NOT_RESCALEDthese last N arguments will not be scaled =5 NBINcompulsory keyword
number of bins for gamma grid =5
W0 could not find this keyword =1000 BIASFACTORcompulsory keyword
bias factor =100.0 BSTRIDEcompulsory keyword
stride for writing bias =2000 BFILEcompulsory keyword
file name for bias =bias.dat
...
PRINT FILEthe name of the file on which to output these quantities =COLVAR ARGthe input for this action is the scalar output from one or more other actions. =* STRIDEcompulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output =100

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 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 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... NOT_SHARED list of arguments (from 1 to N) not summed across replicas NOT_RESCALED these last N arguments will not be scaled MC_STEPS number of MC steps MC_STRIDE MC stride PACE Pace for adding bias, in MC stride unit