different seeds and protein behavior

From: Dr. Eddie (eackad_at_gmail.com)
Date: Thu Jul 19 2012 - 18:29:21 CDT

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.


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