[gmx-users] Asymmetry in homo dimer simulation

[Kavyashree M]

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).

As you have mentioned I do not have replicates of simulations
hence only one 50ns simulation per temperature.

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 <jalemkul at 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
>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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