I don't know the details of what you've done or how you've evaluated
convergence, but I think to answer the questions you pose you'd need to
have well-defined precision. I would want to see more than 1 run for each
simulation method, and comparison to show that the ensembles match even
with different initial coordinates. Only differences larger than
well-designed error bars are meaningful. In other words, we don't have any
idea if the differences you describe are simply run-to-run variation. It's
unlikely that the simulated ensembles that you describe are well converged
even on the microsecond timescale.
===================================================================
Carlos Simmerling, Ph.D.
Professor, Department of Chemistry
Associate Director, Laufer Center for Physical and Quantitative Biology
Laufer Center, Room 119 Phone: 1-631-632-5424
Stony Brook University E-mail:
carlos.simmerling.stonybrook.edu <carlos.simmerling.gmail.com>
Stony Brook, NY 11794-5115 Web: http://www.simmerlinglab.org
===================================================================
On Fri, Apr 12, 2013 at 8:59 AM, Neha Gandhi <n.gandhiau.gmail.com> wrote:
> Dear Amber users and developers,
>
> I have 3 systems with different phosphorylation sites. I am interested in
> secondary structure analyses of these systems. I am using ff10 force field
> with tip3p potential. I started conventional MD with disordered structure
> and after equilibration, ran production for 50ns (NPT) followed by aMD
> (accelerated MD- dual boost potential as implemented in AMBER12.2 GPU
> version) runs upto 300ns.
>
> I also performed conventional MD for 1 microseconds (same force field and
> ensemble as above) which showed that system (1) presence of helical
> structure in the centre; systems (2) and (3) had beta sheets at the N- and
> C-terminals and no helical structure. These analyses from the trajectories
> agree with the experimental data.
>
> The secondary structure analyses obtained from the aMD runs show that all 3
> systems have similar helical structure for last 50 ns. These doesn't
> correlate with experimental data.
>
> How do I interpret these aMD results? What could be the other parameters
> which could be looked that? Does aMD has preference for helical structures
> or is the force field?
>
> Your help is appreciated,
>
>
> --
> Regards,
> Dr. Neha S. Gandhi,
> Curtin Research Fellow,
> School of Biomedical Sciences,
> Curtin University,
> Perth GPO U1987
> Australia
> LinkedIn
> Research Gate
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>
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Received on Fri Apr 12 2013 - 06:30:03 PDT
