AMBER Archive (2008)

Subject: Re: AMBER: Deleting solute from box

From: Bill Ross (
Date: Thu Feb 07 2008 - 15:37:27 CST

> I'm trying to determine the solvated volume of a molecule via a
> two-part calculation: minimization of the solute in an octahedral
> water box, followed by minimization of the system without the solute
> (i.e. just the water molecules).

Minimization of water with the solute removed will not remove the void -
you'd need constant-pressure dynamics to do that.

> I've completed the first calculation to my satisfaction, but am having
> a problem setting up the second one (water only). Can anyone suggest
> a way to remove the solute so I can run MD on the water alone? I
> suspect this is easy, but everything I've tried has caused errors
> (lost the periodic boundaries, etc.)

Why not just build a water box without solute? It would take some
trial and error to get the number of water molecules right, but if
you overshoot by a little you could delete some waters in xleap.

> x = copy WAT
> solvatebox x WATBOX216 15 [starting guess]
> solvatebox x WAT 2 [iteratively add a layer, not sure this will work]
> edit x [delete waters manually]

You may need to just keep trying creating a copy and solvating with
WATBOX216 (if that's still the name of the water box) with different
radii until you get something tractable. Once the desired box is
achieved, equilibrate it under the same conditions that you equilibrated
your solvated system and get the volume from .out (equilibration in
both cases must involve constant pressure at the target temperature).

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