About unwrapping the chain outside the box in periodic boundary condition.

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1

Hi Lammps Users,

I’m simulating using Periodic Boundary Conditions. But the chains usually jump out of the box and into the image box in dump file. Is there any method that I could use to write the dump file into a box but without jumping chains? Or is there any method that I could redefine the box only when I write the coordinate files?

Thanks and looking forward to hearing from you.

Best,
Mingchen.

2

Didn’t Stefan already gave you a suggestion? How did that work for you?

Ray

3

Hi Lammps Users,

I’m simulating using Periodic Boundary Conditions. But the chains usually
jump out of the box and into the image box in dump file. Is there any
method that I could use to write the dump file into a box but without
jumping chains? Or is there any method that I could redefine the box only
when I write the coordinate files?

​this doesn't make sense. the box remains in place during the simulation.
now atoms and molecules will move around unless you have a solid. so them
leaving/entering the simulation box is just normal unless you write out
unwrapped coordinates, which will keep molecules intact, but follow them
through periodic images.

if you want some other behavior, you have to postprocess the trajectory
accordingly.

axel.​