Re: different seeds and protein behavior

Date: Thu Jul 19 2012 - 21:36:23 CDT

Hi.I am not an expert but I have also experienced this. Especially when I have
flexible extended loops, I observe the loops to behave in entirely different
ways on using different seeds. My results were so different that in some runs
the loop folds back to the core of the protein while in some runs it stays
extended for the entire 30ns simulation.


> Hi,
> My colleage and I are having a gentleman's disagreement about MD for
> proteins that I am hoping you experts can solve. If we run MD calculations
> using namd (at constant pressure temperature with an initial minimization
> of 1600 cycles) with same parameters but a different seed we can get
> different "types" of behavior. That is two runs may find that some
> distance-distribution between two residue CA's is centered around some
> value while another two run are centered at a different distance (in the
> 1-2.5 Angstrom range, not too different). In most papers where people
> report results using NAMD they only show one single run. Presumably this is
> because runs with the same parameters (but a different seed) give
> essentially the same result, right?
> We can see this in something large as the full protein's RMSD. Two runs
> will have a RMSD centered nearly the same while two more will have their's
> different by ~1-2 Angstoms (for the backbone CA's). It seems that at 310K
> it is plausible that a protein can have multiple behaviors.Has anyone else
> seen this or is more time required for the protein to stabilize and always
> give a similar result (rmsd, distance distributions etc)? The runs I am
> referring to are done for 16ns.
> Thanks!
> Eddie

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