On Mon, Jun 20, 2016 at 8:18 AM, Jean-Patrick Francoia <
jeanpatrick.francoia.gmail.com> wrote:
> Hi,
>
> Sorry, when I said the box, I meant the box from the isosurface plotting.
>
> My trajectory was obtained in implicit solvent, so no box.
>
> I tried another approach:
>
> center @* origin mass
>
> volmap volmap.dx 0.5 0.5 0.5 .* centermask @*
>
> go
>
>
> And I obtained reasonable densities, as well as the expected spherical
> form.
>
> Is that approach correct ?
>
Yes. If you don't center, then your densities may very well become low if
your system either starts with or picks up any translational motion. The
center command eliminates translations of the center of mass (or geometry).
HTH,
Jason
--
Jason M. Swails
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Received on Mon Jun 20 2016 - 09:00:03 PDT
