Action: TD_GRID

Module	ves
Description	Usage
Target distribution from an external grid file (static).

Details and examples

Target distribution from an external grid file (static).

Using this keyword you can use a target distribution that is read from an external grid file that is in the proper PLUMED file format. You do not to give any information about the external grid file as all relevant information should be automatically detected. It is assumed that the distribution read in from the grid is a proper probability distribution, i.e. always non-negative and can be normalized.

By default the target distribution from the external grid is always normalized inside the code. You can disable this normalization by using DO_NOT_NORMALIZE keyword. However, be warned that this will generally lead to the wrong behavior if the distribution from the external grid is not properly normalized to 1.

If the distribution from the external grid file has for some reason negative values can you use the SHIFT keyword to shift the distribution by a given value. Another option is to use the SHIFT_TO_ZERO keyword to shift the minimum of the distribution to zero.

Note that the number of grid bins used in the external grid file do not have to be the same as used in the bias or action where the target distribution is employed as the code will employ a linear (or bilinear for two dimensions) interpolation to calculate values. Currently only one or two dimensional grids are supported.

It can happen that the intervals on which the target distribution is defined is larger than the intervals covered by the external grid file. In this case the default option is to consider the target distribution as continuous such that values outside the boundary of the external grid file are the same as at the boundary. This can be changed by using the ZERO_OUTSIDE keyword which will make values outside to be taken as zero.

Examples

Generally you only need to provide the the filename of the external grid file.

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

#SETTINGS INPUTFILES=regtest/ves/rt-td-grid/targetdist-input-grid-1d.data INPUTFILELINES=1-20

td: TD_GRIDTarget distribution from an external grid file (static). More details FILEThe name of the external grid file to be used as a target distribution=regtest/ves/rt-td-grid/targetdist-input-grid-1d.data Click here to see an extract from this file.
    ×  FILE: regtest/ves/rt-td-grid/targetdist-input-grid-1d.data
    #! FIELDS arg targetdist
#! SET min_arg -4.0
#! SET max_arg +4.0
#! SET nbins_arg  201
#! SET periodic_arg false
   -4.000000000    0.003777823
   -3.960000000    0.004411205
   -3.920000000    0.005137917
   -3.880000000    0.005969408
   -3.840000000    0.006918146
   -3.800000000    0.007997650
   -3.760000000    0.009222515
   -3.720000000    0.010608418
   -3.680000000    0.012172116
   -3.640000000    0.013931435
   -3.600000000    0.015905227
   -3.560000000    0.018113324
   -3.520000000    0.020576462
   -3.480000000    0.023316186
   -3.440000000    0.026354731
  
The TD_GRID action with label td calculates something

The input grid is then specified using the usual format employed by PLUMED. You can see an example by clicking on the name of the file in the input above.

Full list of keywords

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

Keyword	Type	Default	Description
FILE	compulsory	none	The name of the external grid file to be used as a target distribution
SHIFTThis keyword do not have examples	optional	not used	Shift the grid read in by some constant value
ZERO_OUTSIDEThis keyword do not have examples	optional	false	By default the target distribution is continuous such that values outside the boundary of the external grid file are the same as at the boundary
DO_NOT_NORMALIZEThis keyword do not have examples	optional	false	By default the target distribution from the external grid is always normalized inside the code
WELLTEMPERED_FACTORThis keyword do not have examples	optional	not used	Broaden the target distribution such that it is taken as [p(s)]^(1/gamma) where gamma is the well tempered factor given here
SHIFT_TO_ZEROThis keyword do not have examples	optional	false	Shift the minimum value of the target distribution to zero