On Sun, Apr 8, 2018 at 8:17 PM, Alexander Alexander <alexanderwie...@gmail.com> wrote: > > Thanks Christoph. > > I know they are zero, and > >> <alexand...@gmail.com> wrote: >> > >> > Dear all, >> > >> > The potential_shift.pl crashes in IBI for some of the bond and angles in >> > step 5, I have already seen a suggestion in mailing list such that "one >> > should pick the minimum of the interaction (min property) bigger than 0, >> > so >> > that the target rdf is bigger than 0 as well" (although the crash for >> > this >> > old discussion happened in the step_001). If with minimum of the >> > interaction >> > you mean is the <min>XXXX</min> in the settings.xml file, then it is >> > already >> > more that 0 in may case (<min>2.713</min>). Also in general I did not >> > understand the solutions proposed over there. So, I have attached here >> > some >> > steps of evolution of the problematic angel during IBI, and I would be >> > so >> > appreciated if one could help overcome the problem. >> Looking at your inverse.log: above the error banner "No valid value >> found in angle-H-L-RG.dpot.pure_ibi" >> Looking at angle-H-L-RG.dpot.pure_ibi, all values are marked "o". >> angle-H-L-RG.dist.tgt looks ok, but step_005/angle-H-L-RG.dist.new is all >> zeros. >> So why that is I don't know, but you might want to run csg_stat by hand: > > Yes, they are all zero. > >> >> csg_stat --nt 32 --options >> /home/alex/test/CG/dw/jeffamine-n2/ATB/ibi1/settings.xml --top >> topol.tpr --trj tra >> j.xtc --begin 50 --first-frame 0 --cg >> /home/alex/test/CG/dw/jeffamine-n2/ATB/ibi1/jeffamine2-cg.xml > > Invoking this show nothing again all zero, while invoking this in step_004 > results to a nonzero output. From step 004 to 005 the only thing which > change is the traj.xtc, so it might be something with the mdrun over the > system. My guess is that your system is slowly exploding in step 5 and hence there are no value for the angle in range you specified in the xml file.
Christoph > >> >> (from inverse.log) >> my guess is that something in wrong in jeffamine2-cg.xml, which should >> be a 1:1 mapping on the cg level. > > If that is the case why this does not happen in the steps before? As they > are using the same jeffamine2-cg.xml. > Anyway, I have attached both jeffamine2-cg.xml jeffamine2-aa.xml. > > Best regards, > Alex >> >> Christoph >> > Thank you. >> > Regards, >> > Alex >> > >> > -- >> > 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 votca+un...@googlegroups.com. >> > To post to this group, send email to vo...@googlegroups.com. >> > 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 votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > 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 votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
