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| 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.
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 |
| 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 |
| 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 |
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
1.8.14