Action: ECV_UMBRELLAS_FILE

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

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. The positions $\mathbf{s}_i$ and dimension $\mathbf{\sigma}_i$ of the umbrellas are read from file.

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

Notice that $\mathbf{\sigma}_i$ is diagonal, thus only one SIGMA per CV has to be specified for each umbrella. You can choose the umbrellas manually, or place them on a grid, or along a path, similar to PATH. They must cover all the CV space that one wishes to sample.

The first column of the umbrellas file is always ignored and must be called "time". You can also use as input file a STATE file from an earlier OPES_METAD run (or an OPES_METAD_EXPLORE run, if you combine it with other ECVs).

Similarly to ECV_UMBRELLAS_LINE, you should set the flag ADD_P0 if you think your umbrellas might not properly cover all the CV region relevant for the unbiased distribution. You can also use BARRIER to set the maximum barrier height to be explored, and avoid huge biases at the beginning of your simulation. See also Appendix B of the paper cited below for more details on these last two options.

Examples

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

#SETTINGS INPUTFILES=extras/Umbrellas.data

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
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
cv3The DISTANCE action with label cv3 calculates the following quantities:
 Quantity   
 Type   
 Description  
cv3
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=4,1
ecvThe ECV_UMBRELLAS_FILE action with label ecv calculates the following quantities:
 Quantity   
 Type   
 Description  
ecv.cv1
scalar
the value of the argument named cv1
ecv.cv2
scalar
the value of the argument named cv2
ecv.cv3
scalar
the value of the argument named cv3: ECV_UMBRELLAS_FILETarget 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,cv2,cv3
   FILEthe name of the file containing the umbrellas=
extras/Umbrellas.data
 Click here to see an extract from this file.
  
  ×  
FILE: extras/Umbrellas.data
    
#! FIELDS time cv1 cv2 cv3 sigma_cv1 sigma_cv2 sigma_cv3
1  1.17958  2.93697  1.06109  0.19707  0.28275  0.32427
2  2.04023  2.69714  1.84770  0.22307  0.25933  0.31783
3  1.99693  1.10299  1.13351  0.19517  0.26260  0.37427
4  1.15954  1.37447  2.25975  0.20096  0.27168  0.33353
5  1.10126  2.45936  2.40260  0.19747  0.24215  0.35523
  
   ADD_P0 add the unbiased Boltzmann distribution to the target distribution, to make sure to sample it BARRIERa guess of the free energy barrier to be overcome (better to stay higher than lower)=70
...
ecv: ECV_UMBRELLAS_FILETarget 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,cv2,cv3
   FILEthe name of the file containing the umbrellas=
extras/Umbrellas.data
 Click here to see an extract from this file.
  
  ×  
FILE: extras/Umbrellas.data
    
#! FIELDS time cv1 cv2 cv3 sigma_cv1 sigma_cv2 sigma_cv3
1  1.17958  2.93697  1.06109  0.19707  0.28275  0.32427
2  2.04023  2.69714  1.84770  0.22307  0.25933  0.31783
3  1.99693  1.10299  1.13351  0.19517  0.26260  0.37427
4  1.15954  1.37447  2.25975  0.20096  0.27168  0.33353
5  1.10126  2.45936  2.40260  0.19747  0.24215  0.35523
  
   ADD_P0 add the unbiased Boltzmann distribution to the target distribution, to make sure to sample it BARRIERa guess of the free energy barrier to be overcome (better to stay higher than lower)=70
 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
PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=500 ARGthe labels of the values that you would like to print to the file=cv1,cv2,cv3,opes.bias

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 scalar values that are input to this action

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 scalar values that are input to this action
TEMP	compulsory	-1	temperature
FILE	compulsory	none	the name of the file containing the umbrellas
NUMERICAL_DERIVATIVESThis keyword do not have examples	optional	false	calculate the derivatives for these quantities numerically
BARRIER	optional	not used	a guess of the free energy barrier to be overcome (better to stay higher than lower)
ADD_P0	optional	false	add the unbiased Boltzmann distribution to the target distribution, to make sure to sample it
LOWER_HALF_ONLYThis keyword do not have examples	optional	false	use only the lower half of each umbrella potentials

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)