Hi,
I’ve read the LAMMPS manual, which states Initial coordinates are stored in “unwrapped” form, by using the image flags associated with each atom. See the dump custom command for a discussion of “unwrapped” coordinates. See the Atoms section of the read_data command for a discussion of image flags and how they are set for each atom. You can reset the image flags (e.g. to 0) before invoking this compute by using the set image command.
I am trying to calculate the diffusion of carbon dioxide in a polymer using the MSD command. For this, I am using the output from my sorption simulations as input parameters for an NVT ensemble. However, I would like my atoms to remain wrapped to avoid errors in the results. Could you advise on the correct procedure for this?
Specifically, if I use the read_data command followed by the set group co2 image 0 0 0 command, will this ensure that the MSD command correctly calculates the diffusion? Or is there something else I should do?