Hi Andrey, The initial parameter file *.param.init for the B-spline potential function contains break-points in the first column and knot values in the second column.
As you observed in csg-tutorial/spce/re/ example, the initial values for the knot values can be set to the PMF obtained by inverting the target RDFs, i.e., c_i = -kTlog(g(r_i)). I have found this approach of initializing knot values work well in my RE coarse-graining experiments. Best, Sikandar On Wed, Jul 18, 2018 at 4:42 PM 'Andrey Brukhno' via votca < [email protected]> wrote: > 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 >>> >> -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
