Equilibration (part 4)
Following the examples before, I extracted the temperature from the output files and combined them into one continuous plot. We can see that the temperature has definitely reached the desired 300K after the initial 20 ps of equilibration. For the remaining 100 ps of equilibration, the temperature stayed fairly constant.
During the initial stage of an MD, if the conformation of the molecule is not in a stationary phase, the potential energy can drift around, so the potential energy is typically used as a criteria to decide how much equilibration is needed before production data can be collected and analyzed. Another measure used to help make this determination is the RMSD against the initial structure. Since the potential energy values can be directly extracted from the output file just like the temperature values, I will just go ahead and show you the result.
Next, I will show you how to perform the RMSD calculation using the program ptraj.