*Thank you for getting back to me. I have a few more questions.*
your log files are missing crucial information. please do not use the "log"
command and keep the input commands echoed to the log file.
*What information is missing from my log files? I also have log.lammps file
(which has input commands).*
your npt simulation has very large volume oscillations. that means, either
your choice of time constant is bad, i.e. make it (much) larger and
consider using the 'drag" option as well.
*What do you mean by time constant? Are you referring to Tdamp, Pdamp
parameters of fix npt command?*
*I will look into the "drag" option and try it with a small value of Df.*
*Also, do you think that changing the volume of the box (both in packmol
and lammps input file) so that the molecules' packing is closer to the
target density might help?*