2016-05-20 7:17 GMT-06:00 Takahiro Ohkuma <[email protected]>:
>
>
> 2016年5月19日木曜日 19時20分44秒 UTC+2 Christoph Junghans:
>>
>> 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.
>
> Yes, I would try to do this. Could you tell me the place of codes in which
> the histograms and potentials are computed during ibi?
> tools/src/libtools/histogram.cc?
Have a look here:
<https://github.com/votca/csg/blob/master/src/tools/csg_stat_imc.cc#L283>
Christoph
>
> Takahiro
>>
>>
>> > 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
>> >> >> >> > 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.
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >> --
>> >> >> >> 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 [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
>> >> >
>> >> > --
>> >> > 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.
>> >>
>> >>
>> >>
>> >> --
>> >> 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 [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
>
>
> 2016年5月19日木曜日 19時20分44秒 UTC+2 Christoph Junghans:
>>
>> 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
>> >> >> >> > 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.
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >> --
>> >> >> >> 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 [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
>> >> >
>> >> > --
>> >> > 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.
>> >>
>> >>
>> >>
>> >> --
>> >> 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 [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
>
> --
> 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.
--
Christoph Junghans
Web: http://www.compphys.de
--
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