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=${prefix} -ud
tools csg" in a new directory.
2) The two files of interaction.h and csg_stat_imc.cc files are replaced
with your patch.
3) I typed again "./build.sh --prefix=${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?
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]
> <javascript:>>:
> > 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
> >> >> >
> >> >> > --
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> >> >> > 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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