Periodic boundary conditions

[Dawid das]

Dear CP2K Users,

I am doing QM/MM MD simulation using PBC only for MM part (the QM cell is 
not periodic). My cell is 
orthorombic and I am a bit surprised as in course of simulation some water 
molecules drift away to vacuum 
when I use VMD to visualize my trajectory.

Now, I am aware that if PBC work it does not matter as the image of this 
molecule "enters on the other side"
however this visualization makes me to ask a question whether I do my setup 
correctly.

So in course of MD what I get in XYZ trajectory file is not wrapped by CP2K 
and can I safely wrap those 
molecules/atoms later on with a script? In other words, does CP2K save only 
coordinates of molecules 
found in starting geometry but not its images as they leave the box?

Best wishes,
Dawid

PS This is part of my input that should simply apply PBC, am I right?

  &MM
    &POISSON
      PERIODIC XYZ
      POISSON_SOLVER PERIODIC
      &EWALD
        EWALD_TYPE SPME
!3.5/12 Angstrom
        ALPHA .292
        GMAX  32 32 16
        EWALD_ACCURACY 1.0E-6
      &END EWALD
    &END POISSON
  &END MM

  &SUBSYS
    &CELL
      ABC [nm] 7.60236   6.53052   6.03591
      ALPHA_BETA_GAMMA 90 90 90
      PERIODIC XYZ
!     SYMMETRY ORTHORHOMBIC
    &END CELL

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