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
--
========================================
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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