[CP2K-user] Atom Indices Reorderd

[Rahul Verma]

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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