[gmx-users] Regarding RMSD analysis result

[ahmet yıldırım]

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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