4. Production
Congratulations! After all that hard work, you have finally reached the easy part.
At this stage, you basically use the same protocal as in the final stage of equilibration and simply continue to run the simulation until either you are satisfied or run out of computer time.
Once again, the input file is:
&cntrl
nstlim=500000, dt=0.002, ntx=5, irest=1, ntpr=500, ntwr=5000, ntwx=5000,
temp0=300.0, ntt=1, tautp=2.0,
ntb=2, ntp=1,
ntc=2, ntf=2,
nrespa=1,
&end
Notice that I have increased the number of time steps to 500,000 steps. One decision you need to make here is how long do you want to run? These days, nanosecond length simulations are typically required for publication level work. If you intend to collect several nanoseconds of production data, it is a good idea to pace yourself and resist the urge to run the entire simulation all at once. It is all too easy to "submit and forget". Keeping a vigilant eye on the progress of your simulation may seem a lot of work, but in the end, it will really save you from wasting a lot of time and unnecessary agony.