Hi Sikandar, Thanks for confirming my conclusion about the CG-CG.param.init file.
Would you be able to comment on my question regarding the Sci-Py class BSplines? Best regards Andrey On Thursday, July 19, 2018 at 3:51:53 AM UTC+1, sikandar wrote: > > 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] <javascript:>> 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] <javascript:>. >> To post to this group, send email to [email protected] <javascript:> >> . >> 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.
