On Thu, 2014-05-08 at 13:50 +0300, George Patargias 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.
The "bounding box for atom centers" is exactly that -- it is the
smallest possible box that encloses the _center_ of every single atom in
your system.
The "vdw box size" is a box constructed based on the assumption that
every atom has a size defined by its van der Waals radius. This box,
then, is the smallest box that encloses every *entire* atom not just its
nucleus.
To put it (probably too) simply, the former is a box that encloses all
nuclei, whereas the latter also encloses the electron cloud.*
Note that the vdW box size tends to overestimate the volume, which is
why the starting density for Amber simulations are so low. It does
reduce the chance of having a periodicity-induced clash at the start of
the calculation, though.
HTH,
Jason
*This statement would make a quantum chemist cringe, but hopefully you
get the idea.
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu May 08 2014 - 04:30:04 PDT
