Re: [AMBER] different number of waters

From: newamber list <>
Date: Wed, 18 Jun 2014 14:43:34 +0100

Hi All

Thanks for you replies. Yes I agree choosing same number of water and box
shape initially should converge to similar final equilibrated densities and
volumes with Amber and Gromacs. But I would like to know how AMBER differs
in adding waters compared to Gromacs as a initial guess (earlier I copied
mail from Gromacs archive explaining how initial water box is created by


On Sun, Jun 15, 2014 at 4:52 PM, David A Case <>

> On Sun, Jun 15, 2014, newamber list wrote:
> > command: solvateoct hex20 TIP3PBOX 12.0
> Note that this command is only intended to give a *very rough* starting
> structure for further simulation. The number of water molecules chosen
> for a
> given box size (or buffer size) will be very different from what you will
> get
> after equilibration: the number of waters will stay the same (of course),
> but
> the size of the box will change a lot.
> If you choose the same number of waters in Gromacs and Amber, and simulate
> to
> equilibrium at some temperature, you should get the same average properties
> (such as density). In Amber, at least, the equilibrated density will be
> very
> different than the initial density. No one in the Amber community has not
> (yet) felt a big need to improve the initial guess that LEaP provides.
> ....dac
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Received on Wed Jun 18 2014 - 07:00:02 PDT
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