[email protected] wrote:
Hi All,
I just wanted to let you know how I resolved my problem, in case anyone
else experiences a similar problem in the future.
My structure spanned all four quadrants around the origin (i.e. the 4
vertices of my structure were (-x, -y), (-x,y), (x,-y), & (x,y)). I
think because it spanned all 4 quandrants, this caused the molecule to
jump from corner to corner within the box.
Once I translated my molecule such that its coordinates were entirely
within the positive x,y quandrant, the molecule no longer jumped around
in the box.
...only because the critical feature of the molecule (COM? first atom?)
didn't drift outside the box in which you placed it. I don't know (or
care) what the conventions of GROMACS or your visualization program are,
but the general solution is to forget about it until you go to visualize
your trajectory, and then fiddle with trjconv until you're happy with
the result. :-)
Mark
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