I have created several graphs using NAMD/VMD. The simulation is done using CHARM. The first graphs plots the evolution of the bond energy at timesteps of 2 fm. What I am having difficulty understanding is why there is such chaotic behavior in the first few timesteps. Am I correct in thinking that this highly fluctuating period is exactly the same as the minimization period? And if it IS the minimization that is causing this chaotic behavior, WHY is minimization causing it? I do not see the connection. And the trend is SLIGHTLY upwards -- the trajectory seems to be going from 200 kcal/mol to 250 kcal/mol. The molecule I am modelling is UBIQUITIN. Why is the graph going up? This is where the graph for BOND versus timestep can be found:
https://postimg.org/image/4m7amsy09/
My second question is, the van der Waals force goes WAY down (see the graph in the URL below) in the first few timesteps. Can someone please tell me WHY exactly there is this huge decline in VDW force at the beginning. And once the chaotic behavior has leveled off, there seems to be a stable period where VDW is oscillating on a regular basis. Can someone please tell me WHY and WHEN this stable period begins? Does it begin when equilibration has ended? And WHY does it happen? If anyone could shed light on these two issues, I would be grateful. I am a bit lost.
