[gmx-users] Regarding RMSD analysis result

[Tsjerk Wassenaar]

Hi Ahmet,

What exactly is the RMSD? Well, it's the average distance between
corresponding particles in two structures. So, an RMSD of 2 nm means
that, on average, each particle moved by 2 nm. How large is your
protein at the start? How likely is it that you have such differences
on average, after superposition?

You can also look at it in a different way. The RMSD between two
structures is the difference between the radii of gyration and the
'correspondence'; think of distance: (a-b)^2 = a^2 + b^2 - 2ab. Thus,
the upper limit of the RMSD by definition is equal to the sum of the
radii of gyration. Those shouldn't change too much from the crystal
structure, so you can make an estimate of what you can expect based on
that. Of course, you'll only get the upper bound if there is no
correspondence whatsoever. For a protein, that is impossible, because
of the order and spatial correlation imposed by the bonds.

Hope it clarifies a bit...

Cheers,

Tsjerk

On Tue, Sep 25, 2012 at 7:10 AM, ahmet yıldırım <ahmedo047 at gmail.com> wrote:
> Dear Tsjerk,
>
> You said "RMSD's above 1 nm are suspect, towards 2 highly likely not
> correct." What is the physical/biological/chemical meaning of what you say?
>
> Greetings
>
> 2012/9/24 Tsjerk Wassenaar <tsjerkw at gmail.com>
>
>> 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
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>
>
>
> --
> Ahmet Yıldırım
> --
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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