Molecules translational motion not observed

Dear all,

I have attached my input script. When I visualize the initial dump files from 1000 to 10,000 timesteps, I could not see the translational motion of molecules with assigned velocity. Why is it so? Kindly help me with the same.

NOTE: In this script I haven’t entered mentioned dump interval 1000. But I have actually checked the same.

Thanking you in advance,


new22.txt (3.64 KB)

cyclopentanol.txt (5.84 KB)

you atoms/molecules do move, but it is not easily visible, since they are far too far apart due to a ridiculously large box for your single molecule and you are using a tiny timestep.
that will result in an extremely low density system and you would have to simulate for half an eternity to reach a meaningful density. you should start from something more realistic. also fix npt/nvt are not good choices, if your system is far away from equilibrium. better to use a dissipative thermostat and a barostat, that can react more effectively (even at the expense of not being 100% statistical mechanical correct). after all, equilibrium is a state function, so it doesn’t matter how you get there.


Got it! Thank you so much, sir.