Action: ECV_UMBRELLAS_LINE

Module	opes
Description	Usage
Target a multiumbrella ensemble, by combining systems each with a parabolic bias potential at a different location.

Input

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

Further details and examples

Target a multiumbrella ensemble, by combining systems each with a parabolic bias potential at a different location.

Any set of collective variables $\mathbf{s}$ can be used as ARG.

$$\Delta u_{\mathbf{s}_i}(\mathbf{s})=\sum_j^{\text{dim}}\frac{([s]_j-[s_i]_j)^2}{2\sigma^2}\, .$$

The Gaussian umbrellas are placed along a line, from CV_MIN to CV_MAX. The umbrellas are placed at a distance SIGMA*SPACING from each other, if you need more flexibility use ECV_UMBRELLAS_FILE. The unbiased fluctuations in the basin usually are a reasonable guess for the value of SIGMA. Typically, a SPACING greater than 1 can lead to faster convergence, by reducing the total number of umbrellas. The umbrellas can be multidimensional, but the CVs dimensions should be rescaled since a single SIGMA must be used.

The keyword BARRIER can be helpful to avoid breaking your system due to a too strong initial bias. If you think the placed umbrellas will not cover the whole unbiased probability distribution you should add it explicitly to the target, with the flag ADD_P0, for more robust convergence. See also Appendix B of the paper cited below for more details on these last two options.

The flag LOWER_HALF_ONLY modifies the ECVs so that they are set to zero when $\mathbf{s}>\mathbf{s}_i$, as in LOWER_WALLS. This can be useful e.g. when the CV used is the ENERGY and one wants to sample a broad range of high energy values, similar to ECV_MULTITHERMAL but with a flat energy distribution as target. By pushing only from below one can avoid too extreme forces that could crash the simulation.

Examples

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

cvThe DISTANCE action with label cv calculates the following quantities:
 Quantity   
 Type   
 Description  
cv
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
ecvThe ECV_UMBRELLAS_LINE action with label ecv calculates the following quantities:
 Quantity   
 Type   
 Description  
ecv.cv
scalar
the value of the argument named cv: ECV_UMBRELLAS_LINETarget a multiumbrella ensemble, by combining systems each with a parabolic bias potential at a different location. This action has hidden defaults. More details ARGthe labels of the scalar values that are input to this action=cv CV_MINthe minimum of the CV range to be explored=1.2 CV_MAXthe maximum of the CV range to be explored=4.3 SIGMAsigma of the umbrella Gaussians=0.5 SPACING the distance between umbrellas, in units of SIGMA=1.5
ecv: ECV_UMBRELLAS_LINETarget a multiumbrella ensemble, by combining systems each with a parabolic bias potential at a different location. This action uses the defaults shown here. More details ARGthe labels of the scalar values that are input to this action=cv CV_MINthe minimum of the CV range to be explored=1.2 CV_MAXthe maximum of the CV range to be explored=4.3 SIGMAsigma of the umbrella Gaussians=0.5 SPACING the distance between umbrellas, in units of SIGMA=1.5  TEMP temperature=-1
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=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.* 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

It is also possible to combine different ECV_UMBRELLAS_LINE to build a grid of CV values that will be sampled. For example the following code will sample a whole 2D region of cv1 and cv2.

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

cv1The DISTANCE action with label cv1 calculates the following quantities:
 Quantity   
 Type   
 Description  
cv1
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
ecv2The ECV_UMBRELLAS_LINE action with label ecv2 calculates the following quantities:
 Quantity   
 Type   
 Description  
ecv2.cv1
scalar
the value of the argument named cv1: ECV_UMBRELLAS_LINETarget a multiumbrella ensemble, by combining systems each with a parabolic bias potential at a different location. This action has hidden defaults. More details ARGthe labels of the scalar values that are input to this action=cv1 CV_MINthe minimum of the CV range to be explored=1.2 CV_MAXthe maximum of the CV range to be explored=4.3 SIGMAsigma of the umbrella Gaussians=0.5
ecv2: ECV_UMBRELLAS_LINETarget a multiumbrella ensemble, by combining systems each with a parabolic bias potential at a different location. This action uses the defaults shown here. More details ARGthe labels of the scalar values that are input to this action=cv1 CV_MINthe minimum of the CV range to be explored=1.2 CV_MAXthe maximum of the CV range to be explored=4.3 SIGMAsigma of the umbrella Gaussians=0.5  TEMP temperature=-1 SPACING the distance between umbrellas, in units of SIGMA=1

cv2The DISTANCE action with label cv2 calculates the following quantities:
 Quantity   
 Type   
 Description  
cv2
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=3,4
ecv1The ECV_UMBRELLAS_LINE action with label ecv1 calculates the following quantities:
 Quantity   
 Type   
 Description  
ecv1.cv2
scalar
the value of the argument named cv2: ECV_UMBRELLAS_LINETarget a multiumbrella ensemble, by combining systems each with a parabolic bias potential at a different location. This action has hidden defaults. More details ARGthe labels of the scalar values that are input to this action=cv2 CV_MINthe minimum of the CV range to be explored=13.8 CV_MAXthe maximum of the CV range to be explored=21.4 SIGMAsigma of the umbrella Gaussians=4.3
ecv1: ECV_UMBRELLAS_LINETarget a multiumbrella ensemble, by combining systems each with a parabolic bias potential at a different location. This action uses the defaults shown here. More details ARGthe labels of the scalar values that are input to this action=cv2 CV_MINthe minimum of the CV range to be explored=13.8 CV_MAXthe maximum of the CV range to be explored=21.4 SIGMAsigma of the umbrella Gaussians=4.3  TEMP temperature=-1 SPACING the distance between umbrellas, in units of SIGMA=1

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=ecv1.*,ecv2.* 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=ecv1.*,ecv2.* 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

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)

Syntax

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