2016-05-19 11:07 GMT-06:00 Takahiro Ohkuma <[email protected]>:
> Dear Christoph
>
> I am really grateful for writing a patch.
> Unfortunately, the patch seems not to help for my problem.
> I obtained almost the same results for the dihedral distribution and the
> inverted potential. They still have jumps at the data ends.
>
> Just to make sure, I would like to write down the way I carried out to
> install your patch.
> 1) I downloaded and install votca via "./build.sh --prefix=${prefix} -ud
> tools csg" in a new directory.
Do 1.) and then
$ cd csg
$ git pull
$ git checkout origin/Dihedral
$ make
$ make install
You might have to do some debugging to find out where the jump comes
from, e.g. add a debug message when a point around -pi gets insert in
the histogram.
> 2) The two files of interaction.h and csg_stat_imc.cc files are replaced
> with your patch.
> 3) I typed again "./build.sh --prefix=${prefix} -ud tools csg" to enable the
> patch.
> 4) I sourced the new VOTCARC.bash before a simulation.
>
> Can I use a simplex method for bonded interactions such as
> Ryckaert-Bellemans functions?
It won't be hard, but you will have to do some coding!
You either need to write a file telling gnuplot how Ryckaert-Bellemans
are made up of cos functions or a parameter translator from VOTCA to
gromacs.
Christoph
>
>
> Best regards
> Takahiro
>
> 2016年5月19日木曜日 0時01分51秒 UTC+2 Christoph Junghans:
>>
>> 2016-05-18 11:56 GMT-06:00 Takahiro Ohkuma <[email protected]>:
>> > Dear Christoph
>> >
>> > Thank you for your suggestions. Unfortunately, I found it was difficult
>> > for
>> > me to find out a clue in the votca source codes.
>> >
>> > In the csg_boltzmann conmmand, I could obtain a smooth profile on
>> > condition
>> > that "periodic = 1". There are no jumps at the data ends.
>> > Is it possible to turn on the periodic option during ibi process?
>> Can you check if the following patch helps:
>>
>> <https://github.com/votca/csg/commit/63f8d822187142dc82f3787dd2211a282e39b85b>
>>
>> Christoph
>> > Or, can Votoca omit two data at both ends during ibi?
>> >
>> > Best regards
>> > Takahiro
>> >
>> >
>> >
>> > 2016年5月12日木曜日 19時07分37秒 UTC+2 Christoph Junghans:
>> >>
>> >> 2016-05-11 10:47 GMT-06:00 Takahiro Ohkuma <[email protected]>:
>> >> > Dear Christoph
>> >> >
>> >> > Thank you very much for your prompt reply!
>> >> > I am doing short simulations becase I have not tried the numbers you
>> >> > suggested. I would like to share the results once I get them.
>> >> >
>> >> > I have seen a similar behavior when I made the dihedral potential
>> >> > through
>> >> > boltzmann inversion by using csg_boltzmann.
>> >> If this is happening in csg_boltzmann as well, it sounds like a
>> >> problem in the histogram class.
>> >>
>> >> > At that time, I clipped the edges as a poorly sampled region.
>> >> >
>> >> > Takahiro
>> >> >
>> >> > 2016年5月11日水曜日 17時17分56秒 UTC+2 Christoph Junghans:
>> >> >>
>> >> >> 2016-05-11 4:35 GMT-06:00 Takahiro Ohkuma <[email protected]>:
>> >> >> > Dear all
>> >> >> >
>> >> >> > I am trying IBI for the bonded interactions of my polymer because
>> >> >> > the
>> >> >> > bonded
>> >> >> > potentials obtained by a single-chain simulation in vacuum did not
>> >> >> > well
>> >> >> > reproduce the bond distributions in the melt.
>> >> >> >
>> >> >> > According to the tutorial of "hexane/ibi_bonded", I made a
>> >> >> > setting.xml
>> >> >> > and
>> >> >> > prepared other files.
>> >> >> > But, at the calculation of dihedral distribution in the IBI steps,
>> >> >> > I
>> >> >> > always
>> >> >> > meet a strange sharp peak at an edge of the distribution (one data
>> >> >> > point) as
>> >> >> > the attached png file. This gives a sharp dihedral potential at
>> >> >> > the
>> >> >> > edge,
>> >> >> > and then the next simulation often diverges.
>> >> >> > Although I tried other values of <min>, <max>, and <step>, the
>> >> >> > situation
>> >> >> > did
>> >> >> > not changed.
>> >> >> > Is there any ways to manage this peak in the setting.xml?
>> >> >> Your settings.xml look correct to me!
>> >> >>
>> >> >> IBI for dihedrals isn't very well test and it looks to me there is
>> >> >> an
>> >> >> issue with boundary conditions, i.e. dihedrals are periodic.
>> >> >> Did you try to set max=-min=2.5, or min=0.5 and max= 2pi-0.5?
>> >> >>
>> >> >> Looking at the distribution, it seems the bug is in csg_stat itself.
>> >> >> I
>> >> >> guess the problem is here:
>> >> >>
>> >> >>
>> >> >> <https://github.com/votca/csg/blob/master/src/tools/csg_stat_imc.cc#L400>
>> >> >> It is marked as a TODO ;-)
>> >> >> However, the normalization should not matter as IBI does a ratio of
>> >> >> the distributions, but for the periodic histograms there might be a
>> >> >> round off error.
>> >> >>
>> >> >> Christoph
>> >> >>
>> >> >>
>> >> >>
>> >> >> >
>> >> >> > Best regards
>> >> >> > Takahiro
>> >> >> >
>> >> >> > --
>> >> >> > You received this message because you are subscribed to the Google
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>> >> >> > "votca" group.
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>> >> >> > 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.
>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >> Christoph Junghans
>> >> >> Web: http://www.compphys.de
>> >> >
>> >> > --
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>> >>
>> >>
>> >>
>> >> --
>> >> Christoph Junghans
>> >> Web: http://www.compphys.de
>> >
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>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>
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