On 12/5/12 11:13 AM, Kavyashree M wrote:
Sir,
Thank you for the reply. Total simulated time is 50ns.
first 4ns is left and only 4-50ns were considered for
rmsf calculations. T1 is 300K and T2 is 363K the protein
being simulated is from Ecoli (mesophilic).
I would suggest you compare different, overlapping blocks of time as a further
assessment of convergence. What motivated the choice of the 4-50 ns time frame?
Simple RMSD stability? While that may be one way to assess convergence, it is
not necessarily definitive. If you analyze your RMSF results over different
times, i.e. 4-50, 10-50, 20-50, etc, how do they compare?
As you have mentioned I do not have replicates of simulations
hence only one 50ns simulation per temperature.
I would encourage you to run more simulations. One trajectory is not
definitive.
-Justin
And this happened in two proteins that I had simulated both
are form mesophilic origin.
Thank you
Kavya
On Wed, Dec 5, 2012 at 9:36 PM, Justin Lemkul <jalem...@vt.edu> wrote:
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
--
==============================**==========
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Department of Biochemistry
Virginia Tech
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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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