[gmx-users] NMA in vaccum or water?

[Bert de Groot]

Ruben Martinez Buey wrote:
> 
> Hi all,
> 
> Sorry, I did not understand right,
> 
> 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
____________________________________________________________________________