'centers' refers to a box drawn around the atom centers. The vdw
will project beyond the box.
'Total vdw' includes the vdw of the atoms.
Bill
"George Patargias" <gpat.bioacademy.gr> wrote:
> Hello
>
> I am trying to understand the SolvateBox command from tleap. Basically, in
> the leap log file there is something called
>
> Total bounding box for atom centers: 157.379 141.515 152.369
>
> this is generated by SolvateBox before the addition of water. While after
> the addition of waters there is
>
> Total vdw box size: 160.332 144.804 155.497 angstroms.
>
> which is actually the box information at the end of the amber coordinate
> file.
>
> Could you please tell me what is the difference between them?
>
> I noticed that the "Total bounding box for atom centers" values are closer
> to the box dimensions created by VMD/solvate (using the same solute-box
> edge and solute-water distance)
>
> Thanks in advance.
>
>
>
>
> Dr. George Patargias
> Postdoctoral Research Fellow
> Biomedical Research Foundation
> Academy of Athens
> 4, Soranou Ephessiou
> 115 27
> Athens
> Greece
>
> Office: +302106597568
>
>
>
>
>
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Received on Thu May 15 2014 - 17:00:02 PDT
