> solvateOct aba TIP3PBOX 12.0
>
> I got
>
> Scaling up box by a factor of 1.300525 to meet diagonal cut criterion
> Solute vdw bounding box: 81.041 46.469 55.176
> Total bounding box for atom centers: 112.254 112.254 112.254
> (box expansion for 'iso' is 87.8%)
> Solvent unit box: 18.774 18.774 18.774
> Volume: 726322.374 A^3 (oct)
> Total mass 401178.704 amu, Density 0.917 g/cc
> Added 19597 residues.
>
> So what does the "scaling up" or "expansion" mean when using octahedral box?
I believe the first scaling up by 1.3 is to allow the clearance from
solute to the diagonal faces of the box. I believe the 'iso' expansion
is what is required to get the desired clearance in all directions and
have an isometric box.
Bill
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Received on Fri Oct 07 2011 - 15:00:02 PDT
