[gmx-users] Regarding RMSD analysis result

[naga sundar]

Dear justin

                   Thanks for ur suggestions

                     While speaking about periodic conditions, I followed
the similar condition for both native and mutant complexes. For native
complexes not any big deviation was observed. So its confirmed that nothing
wrong with periodic conditions. Since all the three mutations were having
high clinical significance, we assuming mutation is the only reason for
this abnormal RMSD behavior.  Sudden big increase in the RMSD was observed
in previous mutational  MD studies.
http://www.sciencedirect.com/science/article/pii/S0006291X08020792.

Overall, all  the factors are supporting our results. So shall we take this
RMSD analysis as good result . Even after repeating the 20 ns MD simulation
two times i got the same results.








On Mon, Sep 24, 2012 at 3:41 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/24/12 6:24 AM, naga sundar wrote:
>
>> Dear gromacs users
>>
>>              We performed MD simulation analysis for native and mutant
>> models of protein-protein complexes. From 20 ns simulation trajectory, we
>> generated RMSD graph for one native and three mutant complexes. For native
>> complex in the entire simulation period, we observed  a constant RMSD
>> (~0.15 to ~ 0.25 nm). But, three mutant complexes
>> showed drastic fluctuation in theRMSD  (~0.15 to ~1.75) plot. We analysed
>> all the 3D structure's in the fluctuated areas observed destruction of
>> protein complexes.
>> All the three mutants were already experimentally analyzed and reported
>> that they are involved in the destruction of protein-protein interactions.
>>
>> Query 1: What may be the reason for sudden rise and fall of the RMSD
>> values
>> in mutant complexes. We are assume its because of the involvement of
>> mutation.
>> Query 2: Is there may any other reasons for drastic fluctuation in the
>> RMSD
>> Query 3: Observed results are rite.
>>
>> Here  iam attaching the RMSD graph for your observation.
>>
>>
>>
> Attachments to the list do not work.  You will have to post a link to a
> file sharing site if you wish to share an image.
>
> Such jumps in RMSD are very suspect.  Since you are dealing with
> protein-protein complexes, accounting for periodicity can be very
> challenging.  Have you properly fit the trajectory such that your protein
> subunits are not jumping across periodic boundaries?  If they are, then
> your results are nothing more than an artifact.  If they are not, then you
> have something more interesting, but a tenfold increase in RMSD is very
> peculiar.
>
> -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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-- 
Regards
N.NagaSundaram