Dear Rajesh Kondabala

There is no general rule for the temperatures, it depends on what you want to do, and asked in this way the question has no answer.

It is likely that at that low temperature the NVT run is similar to an advanced energy minimization. Something like starting from a very low kinetic energy of the atoms to let the system relax a bit and then go for the NpT. But the references should be provided by you, you must search the answer where you read this procedure.

I agree with Nicola Piasentin .

In addition, there is no velocity in the minimization. In my experience, I introduce the velocity after minimization by adding random velocity. Low temperature is preferred to avoid the system becoming unstable and exploding. I also prefer to use fixed volume to avoid the sudden change in the volume because there may be the same area having stronger attraction or repulsion. After the system is equilibrated at a low temperature, we can increase the temperature to the desired temperature and use the preferred ensemble.

Anyway, I don't have literature about it. It is a purely based on the manual of software, experience, and other people's suggestion.

As you are now aware, there is quite a bit of "craft" in the practice of molecular dynamics simulations. If simulations could be run for seconds or even milliseconds, there would be no need for much of this craftmanship. As we are constrained to nanoseconds, or at most microseconds, one makes a concerted effort to gently push away from ground truth--the crystal structure---and into the deeper waters of everything floating freely in an NPT simulation. This is solely to avoid running long segments of your simulations in unphysical or unproductive conformations.

This strategy uses initial minimizations to clear bad contacts between solvating waters introduced into the model and hold ions in place because the force fields do not really represent ion coordination. (Van der Waals and electrostatic forces are spherically symmetric. Octahedral coordination is a geometrical accident in the force field, not an intrinsic property of ionic bonding.) Initial dynamics runs are typically NVT with backbone atoms constrained or fixed to allow side chains to begin softly swaying in the breeze. Subsequently, constraints are released and further NPT simulations are run for 1 fs time steps before production runs at 2 ps commence for the duration.

Some simulations also utilize high and low temperatures as another means of control. Low temperatures effectively constrain the atoms in the crystal structure without having to provide constraint information. High temperatures achieve something approaching longer time steps without resorting to higher-order integrations to maintain fidelity. I rarely found fiddling with the temperature to be of much use and, instead, fiddled with constraints. It is a matter of personal taste to a large degree.

You can examine results reported by other groups in similar molecular systems to see what their practices are. You can also look at tutorials for the codes that you are using. Most developers have something like a "best practices" page that explains some of the curious choices for the various parameters involved in the simulations.