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 
>> > 
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>>
>>
>> -- 
>> Christoph Junghans 
>> Web: http://www.compphys.de 
>>
>

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