[gmx-users] Regarding RMSD analysis result

naga sundar naga25sundar at gmail.com
Mon Sep 24 12:24:19 CEST 2012

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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