[gmx-users] Regarding RMSD analysis result
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
> 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.
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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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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