No experimental results. I think I may go with : "that average structures
over the first and second halves of the simulation are the same, for
example)."
And I don't expect any long time-scale motions
thanking you
On Sat, Nov 29, 2014 at 8:47 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Thu, Nov 27, 2014 at 12:40 PM, Mary Varughese <maryvj1985.gmail.com>
> wrote:
>
> > ok sir,
> > then it would be better to allow the structure to evolve itself,
> adjusting
> > torsions and helical. isn't?
> >
>
> That's what I would do.
>
>
>
> > Sir, could you suggest me any criteria in arriving at a reliable
> structure?
> >
>
> If you have experimental measurements, compare against those. Otherwise,
> just check that your structure is converged (e.g., that average structures
> over the first and second halves of the simulation are the same, for
> example).
>
>
>
> > may be rmsd convergence?
>
>
> RMSD isn't always the best for determining whether a simulation has
> converged (at times it can tell you when one _hasn't_).
>
>
>
> >
> > would you prefer long simulation or multiple in
> >
> > such a case?
> >
>
> Multiple long simulations :). This is a loaded question with differing
> opinions, and it often depends on the system of interest (e.g., are there
> any long time-scale motions?). If you can afford both (and/or construct
> "longer" simulations from shorter ones using techniques like Markov state
> models), I would suggest that approach.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Sat Nov 29 2014 - 05:00:02 PST
