Non-periodic region inside a simulation box with periodic boundary condition

LAMMPS LAMMPS General Discussion
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1

Dear all,

Does anyone know how to create a non-periodic region inside a simulation box with periodic boundary conditions?

I want to build a model in which the MOF is surrounded by water. In the large cubic simulation box (50 * 50 * 50) with periodic boundary conditions, the MOF is located from 12 to 39 in three directions in the centre. The water molecules are randomly distributed in the region except for the region where the MOF is already present.

I used two read_data commands to combine the mof data file and water data file, what I obtained is:

image
image932×803 174 KB

The messy bonds in mof are because it is also periodic, so how to make it non-periodic?

can anyone give me some advice? thank you.

all the best

2

You need to replace the periodic bond with two bonds, one bond on each side, that that saturate the open valence created by removing the bond across the periodic boundary, e.g. bonds to a hydrogen atom (which also must be added).