[gmx-users] Regarding RMSD analysis result

[Justin Lemkul]

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.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow

> 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.
>

Without seeing any evidence from your work, I would not be prepared to agree 
with your conclusions.

-Justin

-- 
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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

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