Many thanks for this Jason!
George
> 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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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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 08 2014 - 08:30:04 PDT
