Hi,
We're having some doubts on how post-processing should be handled during
iterative procedures to get potentials. From the manual of VOTCA
("Post-processing of the potential"), we find three procedures:
Clipping: "Regions with an irregular distribution of samples should be
deleted first [...] Alternatively, manually check the range where the
potential still looks good and is not too noisy and set the flags in the
potential file of the bad parts by hand to o (out of range). Those values
will later be extrapolated and overwritten"
Resampling: "Use the command
csg_resample --in table.pot --out table_resample.pot \ --grid min:step:max
[...] It is important to note that the values min and max don’t correspond
to the minimum and maximum value in the input file, but to the range of
values the potential is desired to cover after extrapolation. Therefore,
values in [min,max] that are not covered in the file are automatically
marked by a flag o (for out of range) for extrapolation in the next step."
Extrapolation: "The following line
csg_call table extrapolate [options] table_resample.pot \
table_extrapolate.pot
calls the extrapolation procedure, which processes the range of values
marked by csg_resample. The input file is table_resample.pot created in the
last step.
After resampling, all values in the potential file that should be used as a
basis for extrapolation are marked with an i, while all values that need
extrapolation are marked by o. [...] The output table_extrapolate.pot of
the extrapolation step can now be used for the coarse-grained run. [...]"
Now, all of this is described as something that you do manually after you
had your final "raw" potential from a procedure like Boltzmann inversion.
However, within an iterative procedure like IBI, I would expect this to be
done for every iteration as well, so it has to be somehow automated in the
procedure -if artefacts or jumps due to poorly sampled regions etc.
accumulated, I fear that something could go wrong. And in fact the VOTCA
manual says "These scripts are the same ones as those used for iterative
methods in chapter 7"
We however don't understand if and how it happens. Looking at 1.3 tutorial
files included in the VOTCA distributions, for the coarse-graining of water
with IBI (spce/ibi) we found this in the settings.xml :
<inverse>
<!-- target distribution (rdf), just give gromas rdf.xvg -->
<target>CG-CG.dist.tgt</target>
<!-- update cycles -->
<do_potential>1</do_potential>
<!-- additional post processing of dU before added to potential -->
<post_update></post_update>
<!-- additional post processing of U after dU added to potential -->
<post_add></post_add>
but the <post_update> and <post_add> tags are empty. We have no idea
therefore:
- if we have to put something there
- if yes, what and where (what is to be done post_update but not post_add,
for example?) Is there some settings.xml with examples of this? What is
usually needed?
Can you give some hint here? Thanks a lot!
Dr. Massimo Sandal
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