Dear Dr. Steinbrecher,
I tried most of the tutorials, and I am still learning more. And I am eager
to learn too.
Thank you a lot for your advice. I will keep all these in mind.
Regards,
Chinsu
On Tue, Sep 20, 2011 at 3:25 PM, <steinbrt.rci.rutgers.edu> wrote:
> Hi,
>
> > To start with, how big a box of water would it take to hold your
> > molecule in its extended shape?
> >
> > I set the water TIP3PBOX 12.0 and explicit solvent. Is it what you asked
> > me
> > about? And when I visualize it in VMD, the water still scattered around
> > the
> > protein (md11_water.png attached). Please correct me if i am wrong.
>
> I think the point here is that your system should fit into the periodic
> box at all stages in the simulation. Say your protein is spherical at
> start and 30A across, that plus 12A water on each side, gives you a
> simulation box of ca. 54x54x54A. If you pull apart your protein, it
> becomes an extended chain, say 150 aar and therefore ca. 750A long. Since
> it has to still fit completely into the simulation box and can freely
> rotate, you now would need an ca. 800x800x800A box (much too big to handle
> normally) to prevent your protein from interacting with itself across the
> boundary conditions.
>
> So a straightforward unfolding simulation in explicit solvent may not be
> feasible at all. You could restrict system rotational diffusion with
> restraints, switch to implicit solvent or use coarse grained models, but
> all these (likely) lead to further problems along the road.
>
> Let me stress again that this sounds like a fairly complicated project for
> which no one can present ready made solutions. You will have to learn a
> lot about simulations to come up with a good solution for this problem.
>
> > Please advice me, and if possible, any more reading suggestions are also
> > appreciated.
>
> If you are new to MD simulations, it is a good idea to do all the Amber
> tutorials and then reproduce a published study similar to what you want to
> do later.
>
> Kind Regards,
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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Received on Tue Sep 20 2011 - 01:00:04 PDT
