I am using VMD to plot a graph of the root mean square deviation of a protein. The output that I get is a graph which does not change at all during the first few frames. And at around the fourth or the fifth frame, there is a sudden spike, and then after that things begin to level off. I am not a biologist and I'd appreciate it if someone could explain this to me. There are dots (representing the frames) and straight lines join these dots. The first few dots are horizontal, meaning RMSD is unchanged. But then, like I said, the RMSD increases in value dramatically. Why? And once it has reached about 1.5 Angstroms, the graph levels off. There are minor "ups" and "downs" in the graph, but it generally stays at about 1.5 Angstroms from from frame zero. Can someone tell me why there is no change in RMSD in frame 0, frame 1, frame 2,etc, and how there is a sudden spike, and why there is a tailing off. Which is the minimization part? Which is the equilibration part? Does frame zero indicate the protein natured or denatured? At what point does the protein folding occur? I assume protein folding happens when equilibration stops? Is the "protein folding" bit where the RMSD levels off? I have read about six different online articles and two of them seem to contradict one another. Where exactly is the minimization portion in the RMSD graph? Is it the first few frames?
That is normal. As any physical system that moves from chaos to normality - your protein modelled "in-vacuum" need to accommodate all interactions in aqueous/lipid system). The entire molecule should be in "flux" and try to converge using several local "minima" depending on your parameter selections. Some great tutorials here: http://www.gromacs.org/Documentation/Terminology/Molecular_Dynamics_Simulations
Can you show a plot?
Khader, thank you so much for your reply, and especially for the link. The Gromacs manuals are very useful, I have just had a look at the first one. I have been relying on multiple websites to get a better understanding of protein conformation and RMSD and minimization and all the rest of it, but the Gromacs manuals which you directed me to bring all the concepts together under one roof. Thanks again.