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.
