[gmx-users] NMA in vaccum or water?

Bert de Groot bgroot at gwdg.de
Fri Feb 14 10:46:17 CET 2003

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? 


> which rcoulomb?

5 nm (or something that is as least as large as the largest distance
in your molecule)



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

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