[gmx-users] Regarding RMSD analysis result

[lloyd riggs]

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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