if you want to run a 100 ns simulation, you will need to modify the topology and simulation commands. By changing the topology command, the NVT and NPT simulations will automatically be set for 100 ns.@

The only parameter you have to change if you want to modify the length of a simulation is the number of nsteps in the .mdp file that you use to compile the run of the simulation. Then you recompile the .tpr file with gmx grompp and you just run the simulation. There is no change to the topology needed at all as the simulation stays the same, e.g., you do not change the box/its content/the nature of the molecules inside etc. There are other ways to change the number of steps if you already compiled the .tpr, notably gmx convert-tpr or overwriting the number of steps of the .tpr on the fly during the run by setting the flag -nsteps in gmx mdrun.

What do you mean with NVT and NPT steps? If you run the standard production simulation in the NPT ensemble and with the typical pipeline: energy minimization -> NVT -> NPT -> production (in whatever ensemble), then the NVT/NPT time shouldn't be changed, supposing that it is long enough to equilibrate the system, and you should just change the number of steps of the production run. You shouldn't do statistics/analysis anyway in the equilibration phase, exception made for checks of characteristic quantities to assert if the system is roughly equilibrated or not. If you integration step is 2fs then you are looking for 50mln steps as 50mln*2fs=100ns.

No, Just define a number of steps in the md.mdp file.

for 100 ns, with time step 0.002, the number of steps will be 50000000.

You just need to update the final production run .mdp file. Specifically the nsteps parameter. Apart from that you do not have to change anything. No need to modify the nvt/npt steps.