Hello Diego--

> 
> Thanks for getting back to me. I have added the -thread_filename
> option and the error in the thread files is now: 

> SystemError: xplor-nih error: PairPot<Kernel>::updateNeighborBin:
> number of atoms changed after construction. 
> 

There is a limitation in the current implementation of RepelPot, that
atoms cannot be added or removed after a RepelPot term is created. In
your case, I believe create_EnsWeights is called afterwards, and it
adds pseudo-atoms to represent ensemble weights. If you move the
RepelPot setup further down in the script, to immediately before the line

bond = AvePot(XplorPot,"BOND")

then this issue should be solved.

Charles

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