On Fri, 2014-09-05 at 12:55 +0100, newamber list wrote:
> Hi All
>
> I am just confused about warning in diffusion command.
>
> "Warning: diffusion command currently only works with orthogonal boxes."
>
> So does this mean it works for only rectangular boxes (alpha, beta, gamma =
> 90) only but manual says something regarding orthorhombic box. I am not
> sure if it works with octahedron box?
>
> Then how one can do it with octahedron box
Pay attention to the entire warning. It should have said something
like:
Warning: diffusion command currently only works with orthogonal boxes.
Warning: imaging will be disabled for this command. This may result in
Warning: large jumps if target molecule is imaged. To counter this please
Warning: use the 'unwrap' command prior to 'diffusion'.
So the solution is to follow the advice there -- use the "unwrap"
command prior to the diffusion command.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Sep 05 2014 - 05:30:03 PDT
