Jason Swails <jason.swails.gmail.com> wrote:
> On Wed, Mar 19, 2014 at 10:01 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> > My idea is that you could get a qualitative view of the possible
> > range of motion of your system to get a feel for how much of it
> > the solvated md was covering. I don't think I would do more than
> > watch the movie for a few minutes and maybe grab some interesting
> > frames for exploratory solvated runs. It's more for creative thought.
> >
>
> I still think it would be better to use GB (or even a distance-dependent
> dielectric) instead of vacuum dynamics. They're roughly the same cost
> computationally and prevent the worst of the vacuum artifacts. I think
> there's too much potential for vacuum dynamics to be qualitatively
> misleading even over short time scales at low temperatures...
GB wasn't available when I was in the field, but I thought it was
expensive. If not, this sounds like a better idea.
> Of course these days it's really not too expensive to run a short
> simulation in full explicit solvent and sample starting conformations from
> that if you have a GPU or two to spare for a few minutes.
The idea is to go beyond whatever a short solvated run would give you,
whatever that is.
Bill
>
> All the best,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Wed Mar 19 2014 - 20:00:02 PDT
