On 12/5/12 10:56 AM, Kavyashree M wrote:
Dear users,
I have simulated a homodimer (both the chains with same number
of amino acids and in same configuration) using gromacs 453 in
OPLSAA force field at 2 different temperatures (say T1 and T2). It
was noticed that the rms fluctuation of chain A differs from chain B
in both the simulations. In one of the temperature (T2) the rmsf of the
protein is supposed to be more compared to the other (T1).
When I compare rmsf of chain A at T1 with chain A at T2 (similarly for
chain B). I observed that it shows opposite behaviour. ie chainB is
having increased fluctuation at T1 than at T2.
But actually i observed that the fluctuation of chain A at T1 resembles
the fluctuation of chain B at T2 (with increased values) and similarly
the fluctuations of chain B at T1 resembles that of chain A fluctuation
at T2 (with increased values).
Is this possible? or is there anything wrong?
Your results would indicate simply that while one protein subunit fluctuates
more, the other becomes somewhat more rigid. That's plausible, but perhaps not
intuitive. Keep in mind that RMSF is very sensitive to whether or not your
simulations are actually converged, and a single trajectory under each condition
is insufficient to make very solid claims about anything. How long are the
simulations? How much of the initial time is being disregarded, and thus how
long are the equilibrated segments of the simulations? How different are T1 and T2?
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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