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.
