I have a simulation box with periodic boundary conditions that I like to expand it in the z direction. I want to create a simulation box like this paper. I am using LAMMPS package and my purpose is to calculate thermal conductivity in the end. My system is polymer and water and in total I have 15660 atoms. I have been told that I can do this by using replicate command or appending the same simulation box several times in the specific direction. However, I am not sure if this can give me what I want. Also, in the mailing list, I saw that for such cases it is been suggested to assemble all the simulation blocks from the scratch and then relax the system However, since I am dealing with polymers and it requires specific density and annealing process, I am not sure how to do such process.
The replicate command is pretty explicit on what it does with its name. It literally replicates the box in each given direction. As said from the documentation:
All properties of the atoms are replicated, including their velocities, which may or may not be desirable. New atom IDs are assigned to new atoms, as are molecule IDs. Bonds and other topology interactions are created between pairs of new atoms as well as between old and new atoms. This is done by using the image flag for each atom to “unwrap” it out of the periodic box before replicating it.
This means that any molecular bond you specify in the original data file that crosses a periodic boundary should be between two atoms with image flags that differ by 1. This will allow the bond to be unwrapped appropriately.
This means that you might have to compute a new velocity distribution and let your polymer system relax at high temperature or long time to decorrelate it from you initial configuration.
It is common practice to put polymer molecules in a low density box and let it converge to higher density through simulation with pressure relaxation. The final density/pressure relation is model dependent. This allows to have sets of random configuration that are totally uncorrelated. You can use several tools such as moltemplate or packmol to produce such configuration. It is not that complicated to make a quick and dirty script that makes such initial configurations for LAMMPS. Other solutions have been developed (see for example this article but this is still a non-trivial question.
