[gmx-users] NMA in vaccum or water?

[Ruben Martinez Buey]

> Hi Bert,

One question more: should I include counter-ions if the protein is charged??
What would be the .mdp input for generate the .tpr for genion?
Thanks a lot,
with best wishes,
Ruben


>
> >
> > 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.
>
> > which Coulumb-type?
>
> cut-off
>
> > which rcoulomb?
>
> 5 nm (or something that is as least as large as the largest distance
> in your molecule)
>
> --
>
> Bert
>
> ____________________________________________________________________________
> Dr. Bert de Groot
>
> Max Planck Institute for Biophysical Chemistry
> Theoretical molecular biophysics group
> Am Fassberg 11
> 37077 Goettingen, Germany
>
> tel: +49-551-2011306, fax: +49-551-2011089
>
> email: bgroot at gwdg.de
> http://www.mpibpc.gwdg.de/abteilungen/071/bgroot
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--
___________________________________________

Rubén Martínez-Buey. PhD student
Protein Function and Structure Dept. Lab. 352
Centro de Investigaciones Biológicas (CIB-CSIC)
C/ Velázquez, 144  28006  MADRID
Tlf: +34-91-561 18 00 ext. 4380
___________________________________________


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