Hi, I am doing Essential Dynamics on a protein (150 residues). The simulation is 100ns long and the RMSD becomes very stable after 25ns. I have gone through the mailing list archives but could not find a precise answer to the following question.
When I calculate the cosine content for the first PC by taking the average structure for fitting using g_covar it gives a very high value ~.8. But when I change the reference structure to the starting structure then I get a cosine value ~.1. I also repeated the same by dividing my trajectory into two equal halves but the cosine value with average structure as a reference is always very high while it is reasonably low with starting structure taken as reference. My question is why the cosine content is dependent on the fitting structure used in g_covar? And, especially, which structure is recommended to use in Essential Dynamics analysis ? Any help is appreciated. Thanks a lot. Regards, Vivek Modi Graduate Student, IITK.
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