Hi Jason
Thanks for reply, yes indeed it prints all these warnings. I was just
confused with the message as it says "only" works with orthogonal box.
I have run without iwrap option so all trajectories are unwrapped already.
So I think should be fine without using unwrap.
thanks
Jio
On Fri, Sep 5, 2014 at 1:09 PM, Jason Swails <jason.swails.gmail.com> wrote:
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Sep 05 2014 - 05:30:04 PDT
