[gmx-users] spherical box
s8026264 at sepahan.iut.ac.ir
Sat Jun 7 09:02:00 CEST 2003
On 05 Jun 2003 10:56:18 +0200, David wrote
> On Thu, 2003-06-05 at 11:12, Anton Feenstra wrote:
> > Erik Lindahl wrote:
> > > Hi,
> > >
> > > No, that's a physical impossibility since there is no crystal class with
> > > spherical symmetry.
> > >
> > > Perhaps you're thinking of 'droplet' boundary conditions, but they are
> > > really falling out of popularity compared to accurate Ewald summation in
> > > periodic boxes. We've never bothered to implement it for that reason,
> > > and I doubt we will in the future (it's not difficult for somebody else
> > > to do, though).
> > Using a combination of genbox or genconv, and trjorder it is already quite
> > easy to generate a 'drop' of water. Turning off pbc is also trivial, but
> > there is no straightforward feature to keep water from evaporating into
> > the vacuum. There are also terrible artifacts involved with the water
> > surface, related to dielectric properties and surface tention.
> actually it is still used quite a lot, and new algorithms are being
> developed to deal with it. I'll check the reference...
> > Is there any specific reason why you need this type of system set-up?
> Groeten, David.
> Dr. David van der Spoel, Dept. of Cell and Molecular Biology
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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My reasons is:
I want to consider unfolding a small protein .
there are some limitations for a completely unfolding of the peptide,
if dimention of my box isn't comparable with dimention of the extended
And if I select a big box , I will have more water molecules and so my time of
simulation will be more .
And so I think that it is suitable that use a sherical shell water .
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