Note that there are 2 options for Amber coordinates when you load the
trajectory in the first place:
1. Amber Coordinates
2. Amber Coordinates with Periodic Box
Make sure you pick the right one (try the other one if the first didn't
work).
Good luck,
Jason
On Fri, Jan 14, 2011 at 12:04 PM, Daniel Scott <dscott5.nd.edu> wrote:
> Dear Amber users,
> I am trying out VMD in order to visualize protein dynamics. After loading
> a
> .prmtop file, then a .mdcrd file into it, I have strange bonds that are
> extending out towards the edges of the box....more and more appear as the
> trajectory runs. I assume that this is a periodic box issue...iwrap was
> turned on for the simulation, however (iwrap = 1). How can I eliminate
> these bonds?
>
> Thanks,
> Daniel Scott
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Jan 14 2011 - 09:30:03 PST
