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.
