Dear Thomas,
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.
Currently I only have run about 5000 ps. And I am planning to extend to run another 5000 ps.
For my situation I mentioned above, I think the shrink and expand of the protein molecule is much significant than normal protein molecule, do you agree?
I am looking forward to getting a reply from you.
Cheers,
Acoot
________________________________
From: "steinbrt.rci.rutgers.edu" <steinbrt.rci.rutgers.edu>
To: Acoot Brett <acootbrett.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Friday, 22 June 2012 5:35 PM
Subject: Re: [AMBER] How to explain this phenomenon is production MD
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 Sat Jun 23 2012 - 02:00:07 PDT
