Re: [votca] Re: Initial parameters for RE iteration with 10 potentials
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 <
votca@googlegroups.com> 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
>>>
>> --
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[votca] Re: Initial parameters for RE iteration with 10 potentials
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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[votca] Re: Initial parameters for RE iteration with 10 potentials
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 votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Missing, not found Eigen3 during VOTCA installation
On Wed, Jul 18, 2018 at 12:04 PM, 'Andrey Brukhno' via votca wrote: > Hello, > > The last time I was installing the CSG package in my Ubuntu (up-to-date 2014 > LTS) I got this error from cmake: eigen3 not found, with a suggestion to > provide the path to it. I then downloaded the library from their website, > installed it and added its include directory to both my $PATH and to the > environment under the suggested name EIGEN3_INCLUDE_DIR. But cmake still > complained and stopped with the same error, even when I fed it the flag: > -DEIGEN3_INCLUDE_DIR=. Just a reminder that 2014 was already 4 years ago ;-) We recently fixed an issue in the Eigen3 detection: https://github.com/votca/votca/commit/8fdcedae9b46e1739fa2ef8589cd5a8f6881d420 which includes: https://github.com/votca/tools/commit/3ee8b88e6022772b843f21a04f66a5bd8bfddd09 https://github.com/votca/csg/commit/c3f9b3e2841c4b5c0eac20e4d843f6b108750ecf Did you use that version? > > Not sure what went wrong, but I had to use alternative way of installation > via spack, and it worked eventually, although it lloked like spack installed > ALL the dependencies along with VOTCA in a separate directory, which is of > course an overkill. That is Spack's design, so don't complain to me! And yes we need to update the dependencies of the VOTCA package in Spack. > > I suppose this post is just to notify the current developers that there > might be some issue with finding an exiasting Eigen3 dir. Thanks for letting us know, can you try if above versions fix the issue for you? Christoph > > Thanks > 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 votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- 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 votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
[votca] Missing, not found Eigen3 during VOTCA installation
Hello, The last time I was installing the CSG package in my Ubuntu (up-to-date 2014 LTS) I got this error from cmake: eigen3 not found, with a suggestion to provide the path to it. I then downloaded the library from their website, installed it and added its include directory to both my $PATH and to the environment under the suggested name EIGEN3_INCLUDE_DIR. But cmake still complained and stopped with the same error, even when I fed it the flag: -DEIGEN3_INCLUDE_DIR=. Not sure what went wrong, but I had to use alternative way of installation via spack, and it worked eventually, although it lloked like spack installed ALL the dependencies along with VOTCA in a separate directory, which is of course an overkill. I suppose this post is just to notify the current developers that there might be some issue with finding an exiasting Eigen3 dir. Thanks 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 votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
[votca] Initial parameters for RE iteration with 10 potentials
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 votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
