AMBER Archive (2002)

Subject: Re: minimising WATBOX216

From: Michael G Cooney (chemgc_at_panther.Gsu.EDU)
Date: Tue Jan 15 2002 - 15:38:58 CST

I always minimize and, in some cases, carry out MD on the solvent only, in
order to relax the solvent fully. Although the water box itself is
pre-equilibrated, bad contacts are still possible with the solute. A
procedure called simulated annealing is often done to randomize the water
positions before beginning dynamics. This is explained on the AMBER web
site, www.amber.ucsf.edu/amber/ under tutorials.
Hope this helps.

Sincerely,

Michael G. Cooney, Postdoctoral Associate
Dept. of Chemistry
Georgia State University
Atlanta, GA 30303

On Tue, 15 Jan 2002, sara nunez wrote:

>
>
> I have a macromolecule which I have solvated in a WATBOX216
> in xleap. I understand that the WATBOX216 that xleap is creating
> is an already pre-equilibrated one, and it places the waters in the places
> where there will not be bad contacts. Then, is it necessary to
> run a minimisation of only the solvent molecules with the solute
> fixed? Or is it correct to just start minimising the whole
> complex structure?
>
> Thank you
> s. nunez
>
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