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| 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.
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.
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.
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 arguments if FILE is not found =HILLS.0 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 arguments if FILE is not found =HILLS.1 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 arguments if FILE is not found =HILLS.2 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 arguments if FILE is not found =HILLS.3 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 arguments if FILE is not found =HILLS.4 res: RESCALE ... TEMPcompulsory keyword temperature =300 ARGthe 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 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
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 |
| 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 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 |
1.8.17