Hi,
> I have completed a production MD of a protein, and I find the protein
> shrink and expands repeatedly.
>
> Will you please give me your explanation for this?
Well, from the information you provide we can clearly say that it is
either a natural behaviour of your system, an MD simulation artefact or a
visualisation/analysis problem.
Can you give more details on what exactly is happening, how you measured
it, why your findings are suprising, etc. Otherwise, people who did not
see your results will have difficulties making helpful comments (see
comment above for example).
In the most general sense, I would think that small amplitude 'breathing'
motions are normal in proteins or maybe for this particular one the
conformational change is a functional aspect. It depends on the size of
the changes you see, among other things.
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Fri Jun 22 2012 - 01:00:03 PDT
