On Sunday, April 8, 2018 at 10:17:56 PM UTC-4, Alexander Alexander wrote: > > > Thanks Christoph. > > I know they are zero, and > > <[email protected]> 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. > > >> (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. > > Hello, Here is another example in which this issue happened in the first step, for convenience I share the whole directory, I would be highly appreciated if you could have a look.
https://drive.google.com/open?id=1hvIH9mk1LfYo5LOO1VjBAkBZx7L0q3P0 Thank you. Alex 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 [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.
