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 
> <alexand...@gmail.com <javascript:>> 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. 
>
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 
> >> > 
> >> > -- 
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> >> 
> >> 
> >> 
> >> -- 
> >> Christoph Junghans 
> >> Web: http://www.compphys.de 
> > 
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>
>
> -- 
> Christoph Junghans 
> Web: http://www.compphys.de 
>

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