Re: minimising WATBOX216

From: Michael G Cooney <chemgc_at_panther.Gsu.EDU>
Date: Tue 15 Jan 2002 16:38:58 -0500 (EST)

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, under tutorials.
Hope this helps.


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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Received on Tue Jan 15 2002 - 13:38:58 PST
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