Hi, I just read the message and looked into the files. In my opinion, the issue is the same than above. The file bond-RB-RA.dist.new contains only 0s and therefore dpot.pure_ibi has no valid entries. The setup looks okay to me. I also rerun the gromacs simulation with the tabulated potentials provided in step_001, calculated the RB-RA bond distribution and didn't get all zeros. I'm not exactly sure what happened there.
Best Christoph Am Montag, 9. April 2018 07:09:48 UTC+2 schrieb Alexander Alexander: > > > > On Sunday, April 8, 2018 at 10:17:56 PM UTC-4, Alexander Alexander 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. >> >> >>> (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 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.
