AMBER Archive (2008)

Subject: Re: AMBER: Dimension of the solvated box?

From: David A. Case (case_at_scripps.edu)
Date: Wed Feb 20 2008 - 10:31:36 CST

On Wed, Feb 20, 2008, abiram abiram wrote:
>
> 1) Can somebody tell me which of the line in the above gives the
> dimension of the box.

The "total vdw box size". To double-check, look at the last line of the crd
file you made.

>
> 2) I want to know, whether that dimension is considered as the unit
> cell boxlengths for PBC simulations.

Yes.

>
> 3) Also why there is a large difference in the thrid parameter of
> the lines indicating "Solute vdw bounding box, Total bounding box
> for atom centers, Solvent unit box, Total vdw box size ".

The "solute" is probably not very spherical, as it appears to be about 10 Ang.
longer in the x and y directions than in the z direction. After waters are
added to a certain distance around the solute, the same difference is present.
Using a visualization program to examine your files may help here.

...dac

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