Hi,
> I select 2 specific atoms at each sides of the protein, initially the
> distance between those 2 specific atoms is between the 2 atoms is about 80
> A. After 2000 ps, the distance between those 2 specific atoms changes to
> about 85 A. After about another 2000 ps, the distance between those 2
> specific atoms change backs to about 80 A.
well, that strongly depends on what atoms you select. I think that
movement between 80-85A would be prefectly normal for distant side chains,
but it is much more informative if you visualize your structure, calculate
rmsd values and radius of gyration informations to understand the
conformational changes going on.
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Sat Jun 23 2012 - 04:03:12 PDT
