Thank you axel in respond

Thank you axel in respond

I guess we have to exclude oxygen atoms, because it has long cloumbic

science doesn't work on guesses!

interactions between water molecules and carbon atoms (graphene sheet).

that doesn't make sense in two ways: by excluding interactions between
type 3 atoms, you only affect the water (oxygen) interactions with
itself (i.e. you turn it off) and thus make no change on the water
graphene interaction, and - of course - how can this be a meaningful
model, when you turn real molecules or atoms into what essentially
will behave like an ideal gas?

As I saw simulation process, water molecules completly penetrate from
graphene sheet like there was no obstacle (graphene sheet) for oxygen and
hydrogen atoms passing through!!

that would indicate that your overall setup or choice of parameters or
units is wrong. this most certainly cannot be "cured" by *removing*
interactions through neighbor list exclusion tweaks. who told you to
do this? is there any precedent that you follow.

or somehow I 'm wrong,
How I can create lammps command to make graphene sheet like obstacles with
small pore?

this doesn't look to me as a LAMMPS problem, but a problem of your
understanding of how to set up MD simulations. i suggest you discuss
this with your adviser and get help and advice this way. as has been
observed many times in the past, a mailing list makes for a very bad

what you are trying to do has been done in the past by *lots* of
people and all kinds of different MD codes. so it is not really a
problem of the MD code, but rather of the model and parameters you
feed it. in at least 9 out of 10 cases, if a system doesn't behave
physically, the problem is in the setup and parameter choice and not
in the MD code.