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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Received on Fri Jan 14 2011 - 09:30:02 PST
