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 The ENERGY action with label ene calculates a single scalar value
SELECTOR NAMEcompulsory keyword 
name of the SELECTOR 
=GAMMA VALUEcompulsory keyword 
set (initial) value of the SELECTOR 
=0 The SELECTOR action with label 
res: RESCALE ...
   ARGcompulsory keyword 
the labels of the scalars on which the bias will act 
=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 
...The RESCALE action with label res calculates the following quantities:

 Quantity    Description  
res.bias the instantaneous value of the bias potential
res.igamma gamma parameter
res.accgamma MC acceptance for gamma
res.wtbias well-tempered bias


PRINT FILEthe name of the file on which to output these quantities 
=COLVAR ARGcompulsory keyword 
the labels of the values that you would like to print to the file 
=* STRIDEcompulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output 
=100 The PRINT action with label

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 The ENERGY action with label ene calculates a single scalar value
d: DISTANCE ATOMSthe pair of atom that we are calculating the distance between. 
=1,2 The DISTANCE action with label d calculates a single scalar value
SELECTOR NAMEcompulsory keyword 
name of the SELECTOR 
=GAMMA VALUEcompulsory keyword 
set (initial) value of the SELECTOR 
=0 The SELECTOR action with label 
pbmetad0: PBMETAD ARGcompulsory keyword 
the labels of the scalars on which the bias will act 
=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
arguments if FILE is not found 
=HILLS.0 The PBMETAD action with label pbmetad0 calculates a single scalar value
pbmetad1: PBMETAD ARGcompulsory keyword 
the labels of the scalars on which the bias will act 
=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
arguments if FILE is not found 
=HILLS.1 The PBMETAD action with label pbmetad1 calculates a single scalar value
pbmetad2: PBMETAD ARGcompulsory keyword 
the labels of the scalars on which the bias will act 
=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
arguments if FILE is not found 
=HILLS.2 The PBMETAD action with label pbmetad2 calculates a single scalar value
pbmetad3: PBMETAD ARGcompulsory keyword 
the labels of the scalars on which the bias will act 
=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
arguments if FILE is not found 
=HILLS.3 The PBMETAD action with label pbmetad3 calculates a single scalar value
pbmetad4: PBMETAD ARGcompulsory keyword 
the labels of the scalars on which the bias will act 
=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
arguments if FILE is not found 
=HILLS.4 The PBMETAD action with label pbmetad4 calculates a single scalar value
res: RESCALE ...
   TEMPcompulsory keyword 
temperature =300 
   ARGcompulsory keyword 
the labels of the scalars on which the bias will act 
=ene,pbmetad0.bias,pbmetad1.bias,pbmetad2.bias,pbmetad3.bias,pbmetad4.bias 
   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 
...The RESCALE action with label res calculates the following quantities:

 Quantity    Description  
res.bias the instantaneous value of the bias potential
res.igamma gamma parameter
res.accgamma MC acceptance for gamma
res.wtbias well-tempered bias


PRINT FILEthe name of the file on which to output these quantities 
=COLVAR ARGcompulsory keyword 
the labels of the values that you would like to print to the file 
=* STRIDEcompulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output 
=100 The PRINT action with label

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

ARG	the labels of the scalars on which the bias will act
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
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

Quantity	Description
res.bias	the instantaneous value of the bias potential
res.igamma	gamma parameter
res.accgamma	MC acceptance for gamma
res.wtbias	well-tempered bias