> Note that the vdW box size tends to overestimate the volume, which is
> why the starting density for Amber simulations are so low.
A second reason for this is vdw voids around the solute, due to
the superimpose-then-remove solvation procedure.
Bill
Jason Swails <jason.swails.gmail.com> wrote:
> 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 Mon Jun 02 2014 - 17:30:02 PDT
