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...
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.
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Mar 19 2014 - 19:30:08 PDT
