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 - 00:30:02 PDT
