[gmx-users] shell again

[K.A. Feenstra]

Dmitry Kovalsky wrote:
> 
> On Monday 04 November 2002 13:00, gmx-users-request at gromacs.org wrote:
> 
> > So, you create a 'free space' in between the protein and your water?
> > Why whould you want that?
> 
> As I can understand it is a trick frequently used in MD in order to get faster
> equilibration of system.  (Or I'm wrong?)
> 
> If I use the 'free space' the pressure in system does not jump to 200 or so.
> 
> The case is in width of shell if I use 0.15 it is stable (beacuse only 15
> moleculaes was removed)  if I use 0.3 -- not. Is there any princliples of
> using it ?

I don't really see the point in using it, and I have not heard of other
people using it either. As said, I can see how it would lead to artefacts
and/or problems. I don't quite see how it helps equilibration. I see 
understand your explanation of the sliding puzzle, but the waters don't
really need to change places; they need to find the locally most optimal
orientation and location with respect to the protein surface. Granted,
that might need considerable rearrangement of the hydrogen bonded 
network in the water layer around the protein, but I don't think you
will gain much in that respect by giving the water more space to move
in.

As a final note I would say this: does it take more time to optimize this
accellerated equilibration scheme, or to simply take the non-accelerated
scheme (without the empty layer) and run your simulation some longer...?


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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