Thanks Christoph. I know they are zero, and
<alexand...@gmail.com <javascript:>> 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. 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 <javascript:>. > > To post to this group, send email to vo...@googlegroups.com > <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 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.
jeffamine2-aa.xml
Description: XML document
jeffamine2-cg.xml
Description: XML document
