[gmx-users] Regarding RMSD analysis result

Justin Lemkul jalemkul at vt.edu
Mon Sep 24 12:41:17 CEST 2012

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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