Well, to reduce the burden on the developers' answering (probably obvious
for them) questions, here is what I discovered by simply plotting the
CG-CG.param.init file from the tutorial in csg-tutorials/spce/re/
The CG-CG.param.init file appears to contain the -RT\ln(g_{target}(r)) data
sampled at the spline knots, i.e. the first column is for the knot values
(r) and the second column is the corresponding PMF in kJ/mol - see the
attached plot. I am not sure what is the origin for the slight
discrepancies that are seen in the graph (resampling artefacts?), but it
seems that the mystery about this file has been cleared up.
Andrey
On Wednesday, July 18, 2018 at 10:23:27 PM UTC+1, Andrey Brukhno wrote:
>
> Wow, nobody can answer this straightaway? - I wonder: does this mean that
> no non-associate of the VOTCA team ever used RE method for their actual
> problem (i.e. not a tutorial case)?
>
> Anyway, may I ask those on the team now: in what relation VOTCA's B-spline
> definition is with the corresponding Sci-Py class
> (scipy.interpolate.BSpline)?
>
>
> https://docs.scipy.org/doc/scipy/reference/generated/scipy.interpolate.BSpline.html
>
> I also have another question: what is the actual format of the .param.init
> file? - it is far from being clear in the manual, as the file itself is
> never described.
>
> Thanks again.
>
> Andrey
>
> On Wednesday, July 18, 2018 at 6:51:44 PM UTC+1, Andrey Brukhno wrote:
>>
>> Hello,
>>
>> In an attempt to compare some data obtained with IBI to RE, I am trying
>> to start a relative entropy iteration for the same system. However, I do
>> not know how to generate the initial parameters (aka CG-CG.param.init file)
>> for my system (which would comprise 10 different interaction types).
>>
>> Initially I thought VOTCA would be able to generate the necessary
>> *.param.init files based on my initial potentials provided as *.pot.in
>> (the IBI results) and/or distributions (*.dist.tgt). But it seems not to be
>> the case, as it complaints in the inverse.log about missing *.param.init
>> files.
>>
>> Can anyone suggest a workaround? - I googled and searched here but did
>> not find anything regrading a practical way of creating those files (nor in
>> the manual).
>>
>> Please note: my question is very practical - I know how fit numerical
>> data with regular cubic splines, say in Grace, but VOTCA is using B-splines
>> which are more general (which is good!) but also more involved, so I guess
>> the coefficients of cubic splines cannot be used as initial "guess" for the
>> RE iteration.
>>
>> I essentially need to know what software could do that - ?
>>
>> Thanks in advance!
>>
>> Andrey
>>
>
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