[gmx-users] Longer scale simulations

[David van der Spoel]

On Wed, 2003-12-10 at 14:18, Tsjerk Wassenaar wrote:
> Hi,
> 
> Depending on the geometry of your system and the flexibility, it can be 
> worth performing the simulation in a molecular shaped box. This may save 
> you 50% on computational time. If you like you can contact me off the list.
> 
> You will need a modified version of Gromacs though. I hope these 
> roto-translational constraints make in i
can you be more specific on this stuff? (maybe off the list too). 


> Greetings,
> 
> Tsjerk
> 
> Ran Friedman wrote:
> 
> > Well, that's not very encouraging, but it's better than being wrong!
> >
> > Thanks a lot,
> > Ran.
> >
> > Berk Hess wrote:
> >
> >> >Does this approach still confer some advantages compared to normal MD?
> >> >
> >> >For example, can I use non-periodic boundary conditions in order to 
> >> reduce
> >> >computation time?
> >>
> >> No, it does not.
> >> If you would want to use non-periodic boundary conditions you would 
> >> need to
> >> restrain the outer shell
> >> of solvent atoms, which introduces artifacts. A boundary layer is 
> >> required
> >> to minimize the effect of
> >> these artifacts.
> >> In the end it is computationally cheaper to use a periodic system in a
> >> rhombic dodecahedron box.
> >>
> >> Berk.
> >>
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> >-- 
> >------------------------------------------------------
> >Ran Friedman
> >Laser laboratory for fast reactions in biology
> >Department of biochemistry
> >Faculty of life sciences
> >Tel-Aviv university
> >972-3-6409824
> >------------------------------------------------------
> >
> >  
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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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