I really appreciate your valuable time and consideration.
Regarding energy conservation, my simulation in both serial and parallel reaches a conserved state quickly using minimize command. I did not check with NVE, but I will give it a try and check the energy conservation in NVE.
With respect to my short simulation run (say 200 ps), there are no unusual spikes in energy evolution. I am about to try a longer simulation run to control the energy evolution as well.
Yes, you are right. the easiest way is to start with a small system. I also followed your suggestion and started with a very small case. Now, my small system works and I am going to be certain if everything is Okay before expanding the model.
Best regards,
Majid
