In NVT ensemble, the pressure was not controlled. Thus, it is quite normal that you get high negative value of pressure. In some software such as Gromacs, the pressure value even will not shown if the NVT ensemble was used. Thus, I think that it is okay for NVT ensemble.

If you get strange pressure average in the NPT ensemble, you must be worry about your system, simulation length, and parameter.

Anyway, NVT simulation is not minimization because the system will not minimize. It is a MD simulation. Normally, there is no temperature or velocity in minimization.

Is Desmond run on Windows?

Desmond can be run in windows by installing the ubuntu app from the windows app store. However, you cannot access Desmond GUI. You can run Desmond through command mode.

Thank you for the answer Khabib Khumaini

The pressure inside solids can be a very high negative value meaning you are expanding your system. But when you relax the system with NPT you do not get desired pressure but something fluctuating around meaning expand/ shrink. If you have perfect potential (smooth one with a good tail) you can continue NVT or even NVE and pressure remains constant with much less fluctuations. But if your potential needs some conditions for P to remain constant (like a large cutoff high k-space accuracy and so on), I suggest continuing with NPT because it is less expensive than those conditions. If this is the case, it is worth trying a large damping (some thousands of timesteps) which means you are barostat less frequently. Larger damping is less expensive but it may or may not reduce pressure fluctuations.