Equilibration (Part 3)
By now, I am sure you are beginning to get the hang of it. Once again, we have equilibrated the system for 10 ps and gotten a couple of new output files from the calculation. At this point, our system should have a temperature around 300 K and a density around 1 grams/ml.
Again, let's extract temperature and density data from the output files and plot them.
Excellent! We have brought our system safely from 100 K up to 300 K and adjusted the density of the water box from ~0.8 to ~1.0 grams/ml. To be double sure, we will extend the constant temperature and constant pressure equilibration just a tad longer:
&cntrl
nstlim=50000, 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
Ok, so I understated. We are now going to perform a 100-ps equilibration run. From this point on, unless you have a really fast PC or access to supercomputers, you probably don't want to be sitting around and wait for the results. However, you can still go through the motion of setting up the calculations and let your calculations run for a little while to make sure that you have gotten everything right. I will then supply you with the results so that you can move on to the next step.