AMBER Archive (2008)

Subject: Re: AMBER: setting perioding box in AMBER

From: Vijay Manickam Achari (vjrajamany_at_yahoo.com)
Date: Tue Feb 19 2008 - 00:00:06 CST

Thanks for the reply.
But anyway I have some serious problems here during my equilibrium secession of my bilayer model.
I do minimize my bilayer model in constant volume option.
Than I equilibrated the system in constant pressure.
Once the constrain value become zero, the water enters side part of my simulation and the box size become big.
Is that possible to fix the box so that the water dont get side part of the bilayer?

10kq.

Vijay.M
 
"David A. Case" <case_at_scripps.edu> wrote: On Mon, Feb 18, 2008, Vijay Manickam Achari wrote:
>
> Is that possible in AMBER to determine the box size and shape to our
> preference? Normally we use SETBOX command in xleap to put periodic
> boundary condition. When we use this command , it put rectangle BOX around
> the residue or molecule. If at all we want to define our won shape such as
> monoclinic, is there any way of doing it?

See the "setbox" comand in tleap. Note that this just sets the box, it does
not try to fill it with water or any other solute. You would have to get the
coordinates yourself.

...dac

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Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
 vjramana_at_gmail.com
       
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