[gmx-users] Asymmetry in homo dimer simulation

Justin Lemkul jalemkul at vt.edu
Wed Dec 5 17:16:05 CET 2012

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.


> 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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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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