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. 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] > <javascript:>>: > > 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] <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.
