ECV_UMBRELLAS_FILE

	This is part of the opes module
	It is only available if you configure PLUMED with ./configure –enable-modules=opes . Furthermore, this feature is still being developed so take care when using it and report any problems on the mailing list.

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_MEAD_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 Ref.[60] for more details on these last two options.

Examples

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

cv1: DISTANCE 
ATOMS
the pair of atom that we are calculating the distance between. 
=1,2 The DISTANCE action with label cv1 calculates a single scalar value
cv2: DISTANCE 
ATOMS
the pair of atom that we are calculating the distance between. 
=3,4 The DISTANCE action with label cv2 calculates a single scalar value
cv3: DISTANCE 
ATOMS
the pair of atom that we are calculating the distance between. 
=4,1 The DISTANCE action with label cv3 calculates a single scalar value
ecv: ECV_UMBRELLAS_FILE 
ARG
the input for this action is the scalar output from one or more other actions. 
=cv1,cv2,cv3 
FILE
compulsory keyword 
the name of the file containing the umbrellas 
=Umbrellas.data 
ADD_P0
 could not find this keyword 
 
BARRIER
a guess of the free energy barrier to be overcome (better to stay higher than lower)
=70 The ECV_UMBRELLAS_FILE action with label ecv calculates the following quantities:

 Quantity   
 Description  
ecv.cv1
the label of this action is set by user in the input. See documentation above.
ecv.cv2
the label of this action is set by user in the input. See documentation above.
ecv.cv3
the label of this action is set by user in the input. See documentation above.


opes: OPES_EXPANDED 
ARG
compulsory keyword 
the label of the ECVs that define the expansion. 
=ecv.* 
PACE
compulsory keyword 
how often the bias is updated 
=500 The OPES_EXPANDED action with label opes calculates a single scalar value
PRINT 
FILE
the name of the file on which to output these quantities 
=COLVAR 
STRIDE
compulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output 
=500 
ARG
the input for this action is the scalar output from one or more other actions. 
=cv1,cv2,cv3,opes.bias The PRINT action with label 

The umbrellas file might look like this:

#! 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

Glossary of keywords and components

Compulsory keywords

TEMP	( default=-1 ) temperature. If not specified tries to get it from MD engine
FILE	the name of the file containing the umbrellas

Options

NUMERICAL_DERIVATIVES	( default=off ) calculate the derivatives for these quantities numerically
ADD_P0	( default=off ) add the unbiased Boltzmann distribution to the target distribution, to make sure to sample it
LOWER_HALF_ONLY	( default=off ) use only the lower half of each umbrella potentials
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...
BARRIER	a guess of the free energy barrier to be overcome (better to stay higher than lower)