Action: PROBABILITY_MIX

Module	pathbias
Description	Usage
Mix two frozen path potentials with a fixed global normalization.
output value	type
the complete-path mixed bias energy	scalar

Details and examples

Mix two frozen path potentials with a fixed global normalization.

ARG contains two nonperiodic energy scalars V_c,V_A. The output is -kBT log[(1-eta) exp(-V_c/kBT)+eta exp(-V_A/kBT)/C], where COUPLING is eta in [0,1) and LOG_NORMALIZER is log C. With C=Z_A/Z_c this samples the normalized mixture (1-eta)q_c+eta q_A. An approximate frozen C still defines a conservative potential but changes the actual mixture fraction. C is global, not the coordinate-dependent normalizer of CONDITIONAL_PATH. Derivatives are (1-chi,chi). All replicas must use identical parameters and the same shared full-path inputs. This function neither learns nor biases directly; apply the result using BIASVALUE.

Click on the labels of the actions for more information on what each action computes

cThe DISTANCE action with label c calculates the following quantities:
 Quantity   
 Type   
 Description  
c
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2 NOPBC ignore the periodic boundary conditions when calculating distances
vcThe CUSTOM action with label vc calculates the following quantities:
 Quantity   
 Type   
 Description  
vc
scalar
an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=c FUNCthe function you wish to evaluate=x*x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
vaThe CUSTOM action with label va calculates the following quantities:
 Quantity   
 Type   
 Description  
va
scalar
an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=c FUNCthe function you wish to evaluate=2*x*x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
totalThe PROBABILITY_MIX action with label total calculates the following quantities:
 Quantity   
 Type   
 Description  
total
scalar
the complete-path mixed bias energy: PROBABILITY_MIXMix two frozen path potentials with a fixed global normalization. More details ARGthe labels of the values from which the function is calculated=vc,va KBTpositive thermal energy in the argument energy units=2.5 COUPLINGmixture fraction in [0,1)=0.5 LOG_NORMALIZERfixed dimensionless global log partition-function ratio=0
biasThe BIASVALUE action with label bias calculates the following quantities:
 Quantity   
 Type   
 Description  
bias.bias
scalar
the instantaneous value of the bias potential
bias.total_bias
scalar
one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with  the arguments of the bias followed by the character string _bias. These quantities tell the user how much the bias is due to each of the colvars. This particular component measures this quantity for the input CV named total: BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=total

The example illustrates composition only; its C is not a fitted partition function ratio. KBT and both arguments must use the same energy units. At eta=0 this function returns V_c with derivatives (1,0), but PLUMED still evaluates upstream actions: generate a centroid-only graph to avoid evaluating an invalid or expensive inactive field. Pure V_A is a separate graph.

Input

The arguments that serve as the input for this action are specified using one or more of the keywords in the following table.

Keyword	Type	Description
ARG	scalar	the labels of the values from which the function is calculated

Full list of keywords

The following table describes the keywords and options that can be used with this action

Keyword	Type	Default	Description
ARG	input	none	the labels of the values from which the function is calculated
KBT	compulsory	none	positive thermal energy in the argument energy units
COUPLING	compulsory	none	mixture fraction in [0,1)
LOG_NORMALIZER	compulsory	none	fixed dimensionless global log partition-function ratio
NUMERICAL_DERIVATIVESThis keyword do not have examples	optional	false	calculate the derivatives for these quantities numerically