I have a problem with pbc,

Dear All users

I have a confined system, decane molecules(united atoms) between gold

walls and I did npt ensemble at 300 k and 1 bar,

I attached a snapshot of the last frame in my trajectory file, My simulation box has periodic bc in

x and z direction(blue lines show them) and non periodic bc in y direction(there are decane

molecules between gold layers in this direction) But when my simulation was finished and then I

see my trajectory file in vmd, I saw this event, from 200 ps step some decane molecules went

out my simulation box while in those direction I have periodic boundary condition,

I performed nve and nvt simulation but I got the same result.

Initial size of my gap separation was 40 angs and equilibrated gap separation was 6.5 ang(after equilibration),

0.000000 115.400 xlo xhi
0.000000 60.2 ylo yhi # 0 - 21.2 and 39-60.2 there were my gold layers and 21.2 - 39 there were my decane molecules, for initial configuration,
0.000000 109.933 zlo zhi

How can I solve this problem?

This is my input file,

1.jpg

Dear All users

I have a confined system, decane molecules(united atoms) between gold

walls and I did npt ensemble at 300 k and 1 bar,

I attached a snapshot of the last frame in my trajectory file, My
simulation box has periodic bc in

x and z direction(blue lines show them) and non periodic bc in y
direction(there are decane

molecules between gold layers in this direction) But when my simulation was
finished and then I

see my trajectory file in vmd, I saw this event, from 200 ps step some
decane molecules went

out my simulation box while in those direction I have periodic boundary
condition,

I performed nve and nvt simulation but I got the same result.

where is the problem? this looks perfectly normal.

axel.

Dear Axel

Thank you very much for your reply,

Really? Why do I have some particles out of my boundaries while I have pbc on xz direction.

Size of my simulation box in x y z direction,

0.000000 115.400 xlo xhi
0.000000 60.2 ylo yhi # 0 - 21.2 and 39-60.2 there were my gold layers and 21.2 - 39 there were my decane molecules, for initial configuration,
0.000000 109.933 zlo zhi

But I have some particles in out of this region,

In your opinion, Why do I have this trend when I perform nvt and nve simulation? When I represent the volume of system it is constant,

Dear Axel

Thank you very much for your reply,

Really? Why do I have some particles out of my boundaries while I have pbc
on xz direction.

you have it *because* of periodic boundary conditions.

axel.

Hi Ali,

The periodic boundary conditions are only enforced on updates of the neighbor list. The molecules you see out of your box moved there recently. The minimum image convention makes sure this does not affect the dynamics.

See the first "IMPORTANT NOTE"
http://lammps.sandia.gov/doc/dump.html

Samuel Palato

Hi Ali,

The periodic boundary conditions are only enforced on updates of the
neighbor list. The molecules you see out of your box moved there
recently. The minimum image convention makes sure this does not affect
the dynamics.

no, this is not it. ali just sees "unwrapped" coordinates.

axel.