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Lili Zhang

Atom coordinates in Lammps data file are incorrect

Dear Developers,

The coordinates of atoms in the Lammps data file produced by the simulation choice "Lammps input files only" are not correct. It seems to be the wrapped coordinates, but with no image flags. So some of the bonds that cross the periodic boundaries are overly stretched.

Will it be possible to provide the unwrapped atoms' coordinates in the Lammps data file? 

Many thanks

Lili Zhang


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    Benjamin P Haley

    The coordinates in the LAMMPS data file for the initial structure produced by the builder are correct, but, as you note, they do not have image flags.  LAMMPS cannot store coordinates outside the simulation box, so we can't put the unwrapped coordinates in the LAMMPS input file.  We may be able to add image flags to this file, by adding this capability to the builder and all the tools that process the builder output files to produce a the LAMMPS data file, but this may take a while.  In the meantime, the unwrapped coordinates are available as the "Built structures, unwrapped" output.  You can download the PDB file for the structure.  This file currently does not have the bonds specified, but those could be identified using e.g. OpenBabel.

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