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]
> <javascript:>>:
> > 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?
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] <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.
>
>
>
> --
> 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]
> <javascript:>>:
> > 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] <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.
>
>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
--
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