[gmx-users] Asymmetry in homo dimer simulation

[Kavyashree M]

Sir,

Thank you for your suggestions. I decided the cutoff based on
RMSD convergence. I will calculate at different time intervals.
Running multiple simulation is definitely the best suggestion but
due to time and machine constraint it would be difficult. Instead
I have two mesophilic simulations. But Is there any other way
by which I can prove this point?

Thank you
Kavya

On Wed, Dec 5, 2012 at 9:46 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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 <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://vt.edu/Pages/Personal/justin>
>>> <h**ttp://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
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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