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 The ENERGY action with label ene calculates a single scalar value
SELECTOR 
NAME
compulsory keyword 
name of the SELECTOR 
=GAMMA 
VALUE
compulsory keyword 
set (initial) value of the SELECTOR 
=0 The SELECTOR action with label 
res: RESCALE ...
   
ARG
the input for this action is the scalar output from one or more other actions. 
=ene 
TEMP
compulsory keyword 
temperature 
=300 
   
SELECTOR
compulsory keyword 
name of the SELECTOR used for rescaling 
=GAMMA 
MAX_RESCALE
compulsory keyword 
maximum values for rescaling 
=1.5 
NBIN
compulsory keyword 
number of bins for gamma grid 
=5 
   
W0
 could not find this keyword 
=1000 
BIASFACTOR
compulsory keyword 
bias factor 
=100.0 
BSTRIDE
compulsory keyword 
stride for writing bias 
=2000 
BFILE
compulsory 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 
FILE
the name of the file on which to output these quantities 
=COLVAR 
ARG
the input for this action is the scalar output from one or more other actions. 
=* 
STRIDE
compulsory 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 
ATOMS
the pair of atom that we are calculating the distance between. 
=1,2 The DISTANCE action with label d calculates a single scalar value
SELECTOR 
NAME
compulsory keyword 
name of the SELECTOR 
=GAMMA 
VALUE
compulsory keyword 
set (initial) value of the SELECTOR 
=0 The SELECTOR action with label 
pbmetad0: PBMETAD 
ARG
the input for this action is the scalar output from one or more other actions. 
=d 
SELECTOR
add forces and do update based on the value of SELECTOR 
=GAMMA 
SELECTOR_ID
value of SELECTOR 
=0 
SIGMA
compulsory keyword 
the widths of the Gaussian hills 
=0.1 
PACE
compulsory keyword 
the frequency for hill addition, one for all biases 
=500 
HEIGHT
the height of the Gaussian hills, one for all biases. 
=1 
BIASFACTOR
use well tempered metadynamics with this bias factor, one for all biases. 
=8 
FILE
files 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 
ARG
the input for this action is the scalar output from one or more other actions. 
=d 
SELECTOR
add forces and do update based on the value of SELECTOR 
=GAMMA 
SELECTOR_ID
value of SELECTOR 
=1 
SIGMA
compulsory keyword 
the widths of the Gaussian hills 
=0.1 
PACE
compulsory keyword 
the frequency for hill addition, one for all biases 
=500 
HEIGHT
the height of the Gaussian hills, one for all biases. 
=1 
BIASFACTOR
use well tempered metadynamics with this bias factor, one for all biases. 
=8 
FILE
files 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 
ARG
the input for this action is the scalar output from one or more other actions. 
=d 
SELECTOR
add forces and do update based on the value of SELECTOR 
=GAMMA 
SELECTOR_ID
value of SELECTOR 
=2 
SIGMA
compulsory keyword 
the widths of the Gaussian hills 
=0.1 
PACE
compulsory keyword 
the frequency for hill addition, one for all biases 
=500 
HEIGHT
the height of the Gaussian hills, one for all biases. 
=1 
BIASFACTOR
use well tempered metadynamics with this bias factor, one for all biases. 
=8 
FILE
files 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 
ARG
the input for this action is the scalar output from one or more other actions. 
=d 
SELECTOR
add forces and do update based on the value of SELECTOR 
=GAMMA 
SELECTOR_ID
value of SELECTOR 
=3 
SIGMA
compulsory keyword 
the widths of the Gaussian hills 
=0.1 
PACE
compulsory keyword 
the frequency for hill addition, one for all biases 
=500 
HEIGHT
the height of the Gaussian hills, one for all biases. 
=1 
BIASFACTOR
use well tempered metadynamics with this bias factor, one for all biases. 
=8 
FILE
files 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 
ARG
the input for this action is the scalar output from one or more other actions. 
=d 
SELECTOR
add forces and do update based on the value of SELECTOR 
=GAMMA 
SELECTOR_ID
value of SELECTOR 
=4 
SIGMA
compulsory keyword 
the widths of the Gaussian hills 
=0.1 
PACE
compulsory keyword 
the frequency for hill addition, one for all biases 
=500 
HEIGHT
the height of the Gaussian hills, one for all biases. 
=1 
BIASFACTOR
use well tempered metadynamics with this bias factor, one for all biases. 
=8 
FILE
files 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 ...
   
TEMP
compulsory keyword 
temperature 
=300 
   
ARG
the input for this action is the scalar output from one or more other actions. 
=ene,pbmetad0.bias,pbmetad1.bias,pbmetad2.bias,pbmetad3.bias,pbmetad4.bias 
   
SELECTOR
compulsory keyword 
name of the SELECTOR used for rescaling 
=GAMMA 
MAX_RESCALE
compulsory keyword 
maximum values for rescaling 
=1.5 
NOT_RESCALED
these last N arguments will not be scaled 
=5 
NBIN
compulsory keyword 
number of bins for gamma grid 
=5 
   
W0
 could not find this keyword 
=1000 
BIASFACTOR
compulsory keyword 
bias factor 
=100.0 
BSTRIDE
compulsory keyword 
stride for writing bias 
=2000 
BFILE
compulsory 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 
FILE
the name of the file on which to output these quantities 
=COLVAR 
ARG
the input for this action is the scalar output from one or more other actions. 
=* 
STRIDE
compulsory 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

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