Hi Christoph,

On Thursday, April 19, 2018 at 12:19:49 AM UTC-4, Christoph Junghans wrote:
>
> On Wed, Apr 18, 2018 at 9:39 PM, Alexander Alexander 
> <alexand...@gmail.com <javascript:>> wrote: 
> > Hi 
> > Any ideas please? 
> Sorry, there was no question in your previous email, so I thought it 
> was just FYI. 
>
> Honestly I haven't seen that kind of issue before. 
> Try to set the min of LG-L, LG-LG and LG-H1 a bit higher, e.g. 0.25 or 0.3 
>
Increasing the min can not help, as I tested for another system.

You know, the system has 4 beads LG (G)-H1(H)-L(L)-RG(G) ,inside 
parenthesis are the bead types. And the exclusion defined in cg-mapp.xml is 
as following:
        <name>exclusion</name>
        <beads>
       LG RG
        </beads>
      </bond>
And issue happens wherever LG is involved as I explained earlier.

In a new system which has 5 beads as LG (G)-H1(H)-H2(H)-L(L)-RG(G), for 
which the exclusion defined in cg-mapp.xml is as following:
       <name>exclusion</name>
        <beads>
       LG L
       H1 RG
        </beads>
      </bond>
Now, in the new system, addition to the LG, the problem also happen 
wherever H1 is involved.
The point is that in both systems, the problem shows up for the beads types 
with more than one bead repetition. Like bead type G with LG and RG beads 
in the first system. And types G (beads LG and RG) and H (beads H1 and H2) 
in the second system.
Don't you think somehow the portion of the repetitive bead is missing in 
calculations?

Another question: altering min/max ... in the settings.xml during 
simulation (for instance between step_n and step_n+1) causes crashing the 
job, so how to change them without starting a simulation from scratch?
Thank you.
Regards,
Alex

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

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