I am simulating a box of water molecules which is sandwiched between vapor along z-direction . I am trying to recenter the center of mass of water molecules at z=0 by using fix recenter command. With periodic boundary conditions, I could see the shifting of the water slab and shifting is larger for higher temperatures. However, with non-periodic boundary condition along z-direction, the COM is re-centered at z=0. Is there any other settings or way that I can recenter the COM at z=0 with periodic boundary condition in all directions?
I am not an expert at all with LAMMPS, but I suspect the problem results from molecules transporting across a cell boundary. If that is true, it would be better to fix the momentum of the system. Does LAAMPS have a command for that?
To zero the momentum in LAMMPS:
http://lammps.sandia.gov/doc/fix_momentum.html
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