[gmx-users] Asymmetry in homo dimer simulation

Justin Lemkul jalemkul at vt.edu
Wed Dec 5 17:06:43 CET 2012

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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