[gmx-users] Regarding RMSD analysis result

[Tsjerk Wassenaar]

Hi,

RMSD's above 1 nm are suspect, towards 2 highly likely not correct.
You have to make sure that the molecule is made whole before doing
RMSD analysis.

Cheers,

Tsjerk

On Mon, Sep 24, 2012 at 3:02 PM, lloyd riggs <lloyd.riggs at gmx.ch> wrote:
> You can also just quickly visualize it in VMD and see if anything your looking at is not centred properly.  If it isnt you just have to centre it.
>
> Stephan
>
> -------- Original-Nachricht --------
>> Datum: Mon, 24 Sep 2012 04:32:33 -0700
>> Von: naga sundar <naga25sundar at gmail.com>
>> An: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Betreff: Re: [gmx-users] Regarding RMSD analysis result
>
>> 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
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada