Hi Christoph, On Tuesday, April 10, 2018 at 4:28:30 PM UTC-4, Christoph Junghans wrote: > > On Sun, Apr 8, 2018 at 8:17 PM, Alexander Alexander > <[email protected] <javascript:>> 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. > 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. > Thanks for getting back to me, I am getting such an error over an over now and no success yet just wasting my time. Indeed, even if do not get the potential_shift error, the system crashes at some points later in step_008 or so, with an error like "There is no domain decomposition for" or "bond missing" which are the sign of explosion, even minimization also do not help. But I am sure that the conf.gro comes from a very well equlibrated system (around 9 ns of NVT and NPT equilibrations show a converge density for the system agreeing with experiment), and most importantly, the MD simulation in each step of CG is in NVT ensemble, so, I do not know why explosion should happen in an NVT ensemble.
Would you please let me know the order of potential for a bond like "bond-RB-RA" in each step? I mean for this bond a bond-RB-RA.pot.new will be generated in the step_000, then this bond-A-B.pot.new ---cp--> bond-RB-RA.pot.cur (in step_001) .... . Or in other word, what is the order of the below potential for this bond, which is result of which? bond-RB-RA.dist.new bond-RB-RA.dist.tgt_smooth.ijT3P bond-RB-RA.pot.extrapol.Rh1pt bond-RB-RA.pot.smooth.sXbTa bond-RB-RA.dist.tgt bond-RB-RA.dpot.pure_ibi bond-RB-RA.pot.interpol.0S35s bond-RB-RA.dist.tgt_extrapolated.Q1VJa bond-RB-RA.pot.cur bond-RB-RA.pot.shift.V6IRk Also, which version of gromacs you are using? mine is 2018.1 Best regards, Alex > > 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 [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] <javascript:>. > > To post to this group, send email to [email protected] > <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 [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.
