SE energy calculation with PBC

[shihao]

Dear experts,

I'm trying to run semi-empirical energy calculation using CP2K, but
the calculation was very slow and the system consistency is not very
good. I've tried two systems: one with 125 water molecules (small
system), and the other with 250 water molecules (large system).  To
prepare the large system, we duplicated and shifted the molecules from
the small system to generate two identical adjacent images.  We expect
that the large system will give almost exactly twice the energy as the
small system, but the energies we got are around -1966.78 a.u. and
-3548.09 a.u., respectively, which deviates from 1:2 ratio.  Besides,
the calculations are very slow. In the test of the small system on an
Intel Xeon E5462 quadri-core (3.0 GHz) cpu using one processor, it
took about 8 minutes to finish one inner SCF loop (50 steps).  Is this
expected?

Any help or suggestions will be appreciated.

Thanks.
Shihao

P.S. Here's the input file for the small system test.  I haven't
included the pdb and psf files because there's no upload function now,
but I can send them to you if needed.

@SET CURR_I  01
@SET SEED     1000
&GLOBAL
  PROGRAM_NAME                 CP2K
  PROJECT_NAME                 wt_bk_${CURR_I}
  RUN_TYPE                     ENERGY
  SEED                         ${SEED}
  PREFERRED_FFT_LIBRARY        FFTW
  PRINT_LEVEL                  LOW
  SAVE_MEM
&END GLOBAL

&FORCE_EVAL
  METHOD QS
  &DFT
    &SCF
      SCF_GUESS                ATOMIC
      EPS_SCF                  1.0E-5
      MAX_SCF                  50
      &OUTER_SCF
        MAX_SCF                10
      &END OUTER_SCF
      &PRINT
        &RESTART
          &EACH
            MD                 20
          &END EACH
        &END RESTART
        &RESTART_HISTORY       OFF
        &END RESTART_HISTORY
      &END PRINT
    &END SCF

    &QS
      METHOD                   AM1
      EPS_DEFAULT              1.0E-10
      EXTRAPOLATION            ASPC
      EXTRAPOLATION_ORDER      3
      &SE
      &END SE
    &END QS
    &MGRID
      CUTOFF                   200
    &END MGRID
    &POISSON
      POISSON_SOLVER           PERIODIC
      PERIODIC                 XYZ
    &END POISSON

    &PRINT
      &E_DENSITY_CUBE
        &EACH
          MD                   20
        &END EACH
      &END E_DENSITY_CUBE
    &END PRINT
  &END DFT

  &SUBSYS
    &CELL
      ABC                      15.5516 15.5516 15.5516
      PERIODIC                 XYZ
    &END CELL
    &TOPOLOGY
      CONNECTIVITY             UPSF
      CONN_FILE_NAME           ./build_small.xplor_psf
      COORDINATE               PDB
      COORD_FILE_NAME          ./tip125.pdb
      PARA_RES                 T
    &END TOPOLOGY
  &END SUBSYS
&END FORCE_EVAL