Hi Anna,
did you try to wrap the coordinates back into the original box with ptraj?
water molecules diffuse to the neighboring boxes during a long simulation,
so that it will look like a fuzzy globular shell of waters, although
periodic boundary condition really are in effect and the wrapped
coordinates correspond to a closely packed box.
If this is the sole reason for your problem, then it is just cosmetic,
your simulation did the right thing.
Running this ptraj script will give you a better looking trajectory:
-----------------
trajin <name>
center :<your solute residues> mass origin
image origin center
trajout <name>_img
-----------------
Regards,
Thomas
Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA
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Received on Sun Dec 03 2006 - 06:07:13 PST
