the solvatebox command will build a box using your solute coordinates, and
adding 0 padding (the final value on the solvatebox line) beyond the
solute. So your solute dimensions are defining your box coordinates.
On Fri, Jun 1, 2018 at 1:10 PM, Qinghua Liao <scorpio.liao.gmail.com> wrote:
> Hello everyone,
>
> I am trying to set the water box size, but I failed to get what I want.
>
> For example, I tried to put the protein in a water box with commands:
>
> set mol box {160 160 160}
> solvatebox mol TIP3PBOX 0.0
>
> Then the box information I got is something like this:
>
> Solute vdw bounding box: 160.000 160.000 160.000
> Total bounding box for atom centers: 160.000 160.000 160.000
> Solvent unit box: 18.774 18.774 18.774
> Total vdw box size: 175.760 163.366 162.873 angstroms.
> Volume: 4676619.621 A^3
>
> The box size is 175.760*163.366*162.873 A3, but not 160.0*160.0*160.0 A3
> which is what I expected.
> Could someone tell me how and why the new box size was generated? Thanks
> a lot!
>
>
> All the best,
> Qinghua
>
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Received on Fri Jun 01 2018 - 11:30:01 PDT
