Action: ECV_LINEAR

Module	opes
Description	Usage
Linear expansion, according to a parameter lambda.

Details and examples

Linear expansion, according to a parameter lambda.

This can be used e.g. for thermodynamic integration, or for multibaric simulations, in which case lambda=pressure. It can also be used for multithermal simulations, but for simplicity it is more convenient to use ECV_MULTITHERMAL.

The difference in Hamiltonian $\Delta U$ is expected as ARG.

$$\Delta u_\lambda=\beta \lambda \Delta U\, .$$

Use the DIMENSIONLESS flag to avoid multiplying for the inverse temperature $\beta$.

By defauly the needed steps in lambda are automatically guessed from few initial unbiased MD steps, as descibed in the paper cited below. Otherwise one can set this number with LAMBDA_STEPS. In both cases the steps will be uniformly distriuted. Finally, one can use instead the keyword LAMBDA_SET_ALL and explicitly provide each lambda value.

Examples

Typical multibaric simulation:

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

volThe VOLUME action with label vol calculates the following quantities:
 Quantity   
 Type   
 Description  
vol
scalar
the volume of simulation box: VOLUMECalculate the volume the simulation box. More details
ecvThe ECV_LINEAR action with label ecv calculates the following quantities:
 Quantity   
 Type   
 Description  
ecv.vol
scalar
the value of the argument named vol: ECV_LINEARLinear expansion, according to a parameter lambda. More details ...
  ARGthe label of the Hamiltonian difference=vol
  TEMP temperature=300
  LAMBDA the lambda at which the underlying simulation runs=0.06022140857*2000 #2 kbar
  LAMBDA_MIN the minimum of the lambda range=0.06022140857  #1 bar
  LAMBDA_MAX the maximum of the lambda range=0.06022140857*4000 #4 kbar
...
opesThe OPES_EXPANDED action with label opes calculates the following quantities:
 Quantity   
 Type   
 Description  
opes.bias
scalar
the instantaneous value of the bias potential: OPES_EXPANDEDOn-the-fly probability enhanced sampling with expanded ensembles for the target distribution. This action has hidden defaults. More details ARGthe label of the ECVs that define the expansion=ecv.vol PACEhow often the bias is updated=500
opes: OPES_EXPANDEDOn-the-fly probability enhanced sampling with expanded ensembles for the target distribution. This action uses the defaults shown here. More details ARGthe label of the ECVs that define the expansion=ecv.vol PACEhow often the bias is updated=500  OBSERVATION_STEPS number of unbiased initial PACE steps to collect statistics for initialization=100 FILE a file with the estimate of the relative Delta F for each component of the target and of the global c(t)=DELTAFS PRINT_STRIDE stride for printing to DELTAFS file, in units of PACE=100

Typical thermodynamic integration:

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

DeltaUThe EXTRACV action with label DeltaU calculates the following quantities:
 Quantity   
 Type   
 Description  
DeltaU
scalar
the value of the CV that was passed from the MD code to PLUMED: EXTRACVAllow PLUMED to use collective variables computed in the MD engine. This action is a shortcut. More details NAMEname of the CV as computed by the MD engine=energy_difference
# PLUMED interprets the command:
# DeltaU: EXTRACV NAME=energy_difference
# as follows (Click the red comment above to revert to the short version of the input):
energy_differenceThe PUT action with label energy_difference calculates the following quantities:
 Quantity   
 Type   
 Description  
energy_difference
scalar
the data that was passed from the MD code: PUTPass data into PLUMED More details UNITthe unit of the quantity that is being passed to PLUMED through this value=number SHAPE the shape of the value that is being passed to PLUMED=0 MUTABLE can plumed change the value of the pointer that is passed from the MD code PERIODICif the value being passed to plumed is periodic then you should specify the periodicity of the function=NO
DeltaUThe COMBINE action with label DeltaU calculates the following quantities:
 Quantity   
 Type   
 Description  
DeltaU
scalar
a linear combination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=energy_difference PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- ecvThe ECV_LINEAR action with label ecv calculates the following quantities:
 Quantity   
 Type   
 Description  
ecv.DeltaU
scalar
the value of the argument named DeltaU: ECV_LINEARLinear expansion, according to a parameter lambda. This action has hidden defaults. More details ARGthe label of the Hamiltonian difference=DeltaU TEMP temperature=300
ecv: ECV_LINEARLinear expansion, according to a parameter lambda. This action uses the defaults shown here. More details ARGthe label of the Hamiltonian difference=DeltaU TEMP temperature=300  LAMBDA the lambda at which the underlying simulation runs=0
opesThe OPES_EXPANDED action with label opes calculates the following quantities:
 Quantity   
 Type   
 Description  
opes.bias
scalar
the instantaneous value of the bias potential: OPES_EXPANDEDOn-the-fly probability enhanced sampling with expanded ensembles for the target distribution. This action has hidden defaults. More details ARGthe label of the ECVs that define the expansion=ecv.* PACEhow often the bias is updated=100
opes: OPES_EXPANDEDOn-the-fly probability enhanced sampling with expanded ensembles for the target distribution. This action uses the defaults shown here. More details ARGthe label of the ECVs that define the expansion=ecv.* PACEhow often the bias is updated=100  OBSERVATION_STEPS number of unbiased initial PACE steps to collect statistics for initialization=100 FILE a file with the estimate of the relative Delta F for each component of the target and of the global c(t)=DELTAFS PRINT_STRIDE stride for printing to DELTAFS file, in units of PACE=100

Notice that by defauly LAMBDA=0, LAMBDA_MIN=0 and LAMBDA_MAX=1, which is the typical case for thermodynamic integration.

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 label of the Hamiltonian difference

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 label of the Hamiltonian difference
TEMP	compulsory	-1	temperature
LAMBDA	compulsory	0	the lambda at which the underlying simulation runs
NUMERICAL_DERIVATIVESThis keyword do not have examples	optional	false	calculate the derivatives for these quantities numerically
LAMBDA_MIN	optional	not used	the minimum of the lambda range
LAMBDA_MAX	optional	not used	the maximum of the lambda range
LAMBDA_STEPSThis keyword do not have examples	optional	not used	uniformly place the lambda values, for a total of LAMBDA_STEPS
LAMBDA_SET_ALLThis keyword do not have examples	optional	not used	manually set all the lamdbas
DIMENSIONLESSThis keyword do not have examples	optional	false	ARG is considered dimensionless rather than an energy, thus is not multiplied by beta
GEOM_SPACINGThis keyword do not have examples	optional	false	use geometrical spacing in lambda instead of linear spacing

References

More information about how this action can be used is available in the following articles:

• M. Invernizzi, P. M. Piaggi, M. Parrinello, Unified Approach to Enhanced Sampling. Physical Review X. 10 (2020)