2016-05-23 5:23 GMT-06:00 Takahiro Ohkuma <[email protected]>: > Dear Christoph > > I found a possible way to avoid the jumps in dihedral distributions. > There are 3 points I should notice. > > (1) > The bin range of the histogram is made as [ x - 0.5 * step , x + 0.5 * > step]. > Therefore, when I choose min=-3.14, max=3.14, and step=0.04, the histogram > gets sudden drops at both ends because there are no data in the ranges of > [-3.16, -pi] and [pi, 3.16]. > I think I should choose the values so that "min - 0.5 * step >= -pi" and > "max + 0.5 * step <= pi". > In addition, it is better to make (max - min)/step be integer. If not, the > situation could become more complicated because the bin width of the > histogram seems not to be the same as step value defined in the xml file. > > > (2) > The periodic option should be off. If there are data greater than > max+0.5*step, they are counted in the periodic potion. > For example, if I choose min=-3.12, min=3.12, and step=0.04 with the > periodic option, the histogram again jumps at both data ends by the > populations in [-pi, -3.14] and [3,14, pi]. The magnitude of the jumps is > around 4% because (pi - 3.14)/0.04 ~ 0.0398. > > (3) > There might be a possible bug in line 53 of > tools/src/libtools/histogramnew.cc. I think floor function should be used > instead of int as follows. > i = (int)((v - _min)/ _step + 0.5); > i = (int)floor((v - _min)/ _step + 0.5); > > Because i should be a negative integer if v is less than _min - 0.5*_step. > But, for instance, int(-0.1) = 0 not -1. > This could lead a jump at one end of the histogram because some data are > over-counted as i=0. > I found a similar problem in line 76 of tools/src/libtools/histogram.cc. Thanks for the nice summary, can you try this commit https://github.com/votca/tools/commit/79e67b43eb7eee6ca69051f733643d4a26b81f8d i.e. $ cd tools $ git pull $ git checkout histogram $ make $ make install
Thanks, Christoph > > Best regards > Takahiro > > > 2016年5月20日金曜日 17時08分09秒 UTC+2 Christoph Junghans: >> >> 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 > > -- > 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.
