[CP2K-user] Atom Indices Reorderd

[Marcella Iannuzzi]

Hi Rahul, 

I would try to have cp2k generate a connectivity file first and then base 
the qm/mm input on it,
i.e., passing the connectivity file instead of generating the connectivity 
on the fly.

Best
Marcella


On Friday, July 2, 2021 at 9:10:37 AM UTC+2 rah... at gmail.com wrote:

>
> Hello all,
>        
> I am trying to do a QM/MM molecular dynamics study in which I am using my 
> input structure in xyz format. While running the calculation I encounter an 
> issue that in the trajectory file the atom indices are now being reordered. 
> And because this shuffle in the atom indices, the QM/MM boundary atom index 
> also got changed hence, my capping in not on the correct atoms so the 
> simulation got crashed.
>
> Below is the input Topology section :
>     &TOPOLOGY
>       COORD_FILE_FORMAT xyz
>       COORD_FILE_NAME input.xyz
>       EXCLUDE_VDW 1-1
>       DISABLE_EXCLUSION_LISTS TRUE
>       &GENERATE
>         CREATE_MOLECULES TRUE
>       &END GENERATE
>       &CENTER_COORDINATES
>       &END CENTER_COORDINATES
>     &END TOPOLOGY
>
> Any help would be appreciated.
>
> Regards
> Rahul
>
>
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