AMBER Archive (2008)

Subject: Re: AMBER: Deleting solute from box

From: Kevin Davies (
Date: Thu Feb 07 2008 - 16:21:22 CST

I was planning to just resume MD to deal with the cavity and
(hopefully) bypass the trial-error phase. But your approach sounds
tractable, so I'll go that route. Thanks!

On Feb 7, 2008 4:37 PM, Bill Ross <> wrote:
> > 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).
> Bill
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