TD_GRID

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

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

td: TD_GRID 
FILE
compulsory keyword 
The name of the external grid file to be used as a target distribution. 
=input-grid.data The TD_GRID action with label td

The input grid is then specified using the usual format employed by PLUMED an example of which is shown below:

#! FIELDS d1 external.bias der_d1
#! SET min_d1 1.14
#! SET max_d1 1.32
#! SET nbins_d1 6
#! SET periodic_d1 false
   1.1400   0.0031   0.1101
   1.1700   0.0086   0.2842
   1.2000   0.0222   0.6648
   1.2300   0.0521   1.4068
   1.2600   0.1120   2.6873
   1.2900   0.2199   4.6183
   1.3200   0.3948   7.1055

Glossary of keywords and components

Compulsory keywords

FILE	The name of the external grid file to be used as a target distribution.

Options

ZERO_OUTSIDE	( default=off ) 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. This can be changed by using this flag which will make values outside to be taken as zero.
DO_NOT_NORMALIZE	( default=off ) By default the target distribution from the external grid is always normalized inside the code. You can use this flag to disable this normalization. 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.
SHIFT_TO_ZERO	( default=off ) Shift the minimum value of the target distribution to zero. This can for example be used to avoid negative values in the target distribution. If this option is active the distribution will be automatically normalized.
SHIFT	Shift the grid read in by some constant value. Due to normalization the final shift in the target distribution will generally not be the same as the value given here
WELLTEMPERED_FACTOR	Broaden the target distribution such that it is taken as [p(s)]^(1/ \(\gamma\)) where \(\gamma\) is the well tempered factor given here. If this option is active the distribution will be automatically normalized.