[gmx-users] NMA in vaccum or water?

[David]

On Thu, 2003-02-27 at 05:07, Ruben Martinez Buey wrote:
> >  for energy minimization before NMA, do you recommend water or vacuum?
> >
> >
> > a water shell with 1-2 layers of water molecules (and internal waters),
> > if you can afford the computational effort. Otherwise vacuum.
> > In this article:
> >
> > A.Amadei, B.L. de Groot, M.-A. Ceruso, A. Di Nola and H.J.C. Berendsen;
> > A kinetic model for the internal motions of proteins: Diffusion between multiple
> > harmonic wells , PROTEINS: Struct. Funct. Gen. 35: 283-292 (1999).
> >
> > we saw that including internal waters and an external layer of water
> > molecules gave much more realistic results than vacuum NM.
> >
> 
> OK, but how can I do that (a water shell with 1-2 layers of water molecules (and
> internal waters))?

genbox -shell XXX

> Thanks a lot for your kind attention,
> with best regards,
> Ruben
> 
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-- 
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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