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? 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] > <javascript:>>: > > 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] <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 > -- 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.
