I've checked your files, and indeed, imaginary frequencies present at
the gamma point. The problem however is not related to
the potential used nor to fix-phonon, but that your configuration is not
at its equilibrium state. Although it looks so,
it is however an artifact due to the constraint on cell shape/volume by NVT.
I replaced your:
fix NVT all nvt temp 300 300 0.01
fix NPT all npt temp 300 300 0.01 tri 1. 1. 1.
and then everything went well, no imaginary frequencies anymore.
I cc'ed this message to the lammps mail list in case the other might run
into the same problem.
�� 2013-11-04 17:57, Aris Sgouros д��: