Bond missing in non periodic direction

Dear All users,

I want to investigate how my molecules will interact with the surface which is located at the

the bottom of my simulation box. For this purpose I use slab boundary condition in

z direction ( with f, non-periodic and fixed). I have a problem with bond missing on my two

atoms which go outside of my boundary.

Can I solve this problem by increasing the size of my simulation in z direction and above

my surface? Has any body encountered this problem before?

Dear All users,

I want to investigate how my molecules will interact with the surface which
is located at the

the bottom of my simulation box. For this purpose I use slab boundary
condition in

z direction ( with f, non-periodic and fixed). I have a problem with bond
missing on my two

atoms which go outside of my boundary.

Can I solve this problem by increasing the size of my simulation in z
direction and above

my surface? Has any body encountered this problem before?

lammps offers multiple ways to deal with it. which one is suitable
depends on things only you know. you should by now know that will get
told to read it, look for possible options, experiment and figure out
which is the most suitable. so i wonder why you don't anticipate this
answer and save us the effort to tell you.

axel.

"it" meaning the documentation, of course.

If your atoms go outside a fixed (“f”) boundary
they are deleted from the system. Hence anything
bonded to them will throw an error. See the boundary
doc page for different kinds of boundaries.

Steve

Dear Steve,

Thank you for your reply,

I read it, but I can not be sure about which one I should choose. I tried periodic boundary condition but my atoms sensed another side of my surface and it was

like a confined structure. Besides, I want to perform NVT ensemble and I need a fixed boundary and in case of S, I read this line in doc, I have no idea about what

it means. I want to have all of my molecules in my box:

yes, it means you allow them to go outside the box and the box
grows accordingly.

Steve

Dear Steve,

Thank you very much for your reply.

Therefore, I can not use this type of BC for NVT ensemble because the volume of my simulation box probably will be changed.

Dear Steve,

Thank you very much for your reply.

Therefore, I can not use this type of BC for NVT ensemble because the volume
of my simulation box probably will be changed.

you don't have an nvt ensemble with either "f" or "s" or "m" boundary.

axel.

Dear Steve,

Thank you very much for your reply.

Therefore, I can not use this type of BC for NVT ensemble because the volume
of my simulation box probably will be changed.

you don't have an nvt ensemble with either "f" or "s" or "m" boundary.

...and to preempt the next question. in either case your volume is
infinite. the physics of your system is unchanged, the difference is
more a question of accounting, performance and convenience, i.e.
whether you want to keep track of atoms that fly away or not, and
whether you will be affected by load imbalance issues.

an nvt ensemble requires periodic boundaries. this is *fundamental*
stat. mech. knowledge. you better start working on that, before it is
to late.

axel.

Dear Axel,

Thank you for your reply.

I wanted to ask another question which you answered it.