[gmx-users] Regarding RMSD analysis result
jalemkul at vt.edu
Mon Sep 24 14:04:53 CEST 2012
On 9/24/12 7:32 AM, naga sundar wrote:
> 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
I think you may have misunderstood what I was saying. I was not referring to
the simulation conditions themselves, but rather the normal post-processing of
the trajectory with trjconv to assure a continuous image of the trajectory. If
one subunit crosses a periodic boundary (as a consequence of normal diffusion),
you will see a sudden spike in the RMSD value. You must correct for this effect
using trjconv before running analysis.
> 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.
> 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.
Without seeing any evidence from your work, I would not be prepared to agree
with your conclusions.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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