Interactions between periodic images _Reg

​Dear all,

I am using fix deform to perform uniaxial tension test on all atom type polymer system with 60000 atoms. My box size is xlo xhi -100 100, ylo yhi -100 100, zlo zhi -100 100. I have saved my trajectory information using unwrap command in dcd file format. I am viewing the trajectory file using VMD. I have switched on the periodic images in VMD, During the equilibration process, the polymer chains in the periodic images are close to each other i.e., there is contact between some chains at the edges of boxes. But, while deforming the box, it is observed that the periodic images are moving away from each other after a particular strain % in x direction. There is no interactions between chains in the periodic images.

In this connection, I would like to know:

  1. What type of interactions must be there between periodic images? Whether non bonded interactions are sufficient or should I reduce the box size so that the images overlap each others?

  2. Whether the periodic boxes should be always in contact with each other to symbolize the bulk behaviour?

  3. I am not sure, whether this is going to affect my stress-strain plot.

Thank you,

Dear all,

I am using fix deform to perform uniaxial tension test on all atom type
polymer system with 60000 atoms. My box size is xlo xhi -100 100, ylo yhi
-100 100, zlo zhi -100 100. I have saved my trajectory information
using unwrap command in dcd file format. I am viewing the trajectory file
using VMD. I have switched on the periodic images in VMD, During the
equilibration process, the polymer chains in the periodic images are close
to each other i.e., there is contact between some chains at the edges of
boxes. But, while deforming the box, it is observed that the periodic images
are moving away from each other after a particular strain % in x direction.
There is no interactions between chains in the periodic images.

your interpretation of your visualization is incorrect.
what you are describing is most likely an artefact of using unwrapped
coordinates.
forces are always computed in the principal cell, the unwrapped
coordinates are then generated using image flags. the longer your
simulation, the more your system will diffuse, the more molecules will
be separated.

In this connection, I would like to know:

1. What type of interactions must be there between periodic images? Whether
non bonded interactions are sufficient or should I reduce the box size so
that the images overlap each others?

you need to read up on periodic boundary conditions and how forces are
computed in an MD with PBC.
to get the visualization you desire, you probably need to use pbctools
in VMD to wrap molecules back into the principal cell (but as whole
molecules). LAMMPS cannot do this and you want to avoid more complex
post-processing in VMD, writing out unwrapped coordinates is the right
choice.

2. Whether the periodic boxes should be always in contact with each other to
symbolize the bulk behaviour?
3. I am not sure, whether this is going to affect my stress-strain plot.

i think those questions will answer themselves, once you have updated
your understanding of PBC in MD simulation codes.

axel.