my question is very simple, can i use same timesteps for small or large
system? as per given paper they used 216 particle,npt system and time
step is 0.005 in reduced unit. now i increased my system using 2744
particle, so can i used same time step or i have to change my time
Impossible to say with certainty.
Larger systems permit larger fluctuations.
But you could also simply made a mistake when enlarging the system.
Or have a typo.