[gmx-users] NMA in vaccum or water?

[Ruben Martinez Buey]

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