Remove all atoms equivalent (because of the PBC) to an already defined one, e.g. atom 12 which is equivalent to atom 11. The list of too short distance warning can help you to identify the redundant atoms.
--
You received this message because you are subscribed to the Google Groups "cp2k" group.
To unsubscribe from this group and stop receiving emails from it, send an email to
cp2k+uns...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/3d6046a0-d3a1-4d3f-ba3b-e0cfe273b419n%40googlegroups.com.
That’s something you have to adjust in VMD, i.e. you have to define the maximum distance between atoms for drawing bonds in VMD.
To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/1f319213-2806-457d-b942-7f2db2a33eb3n%40googlegroups.com.