I am interested in a simulation involving a large protein homodimer. In
order to save computational resources it would be ideal if I could simulate
only a single full protein that interacts with its own image across a
periodic boundary; however, for this to work, I would need a way to
"invert" the boundary condition to obtain the desired symmetry. I'm after
something like this (hope the ASCII schematic comes through clearly):
__A__________
| | |
| d|p |
| d|p |
| d|p |
| | |
----------------A'----
Where A on the left is the simulation box containing the protein d,
interacting with the mirror image A' on the right containing a mirror image
of the protein, p.
Is anyone aware of a way to implement this sort of boundary condition in
Amber? Is this more trouble than it's worth?
Thanks!
-Tucker Burgin
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Feb 08 2022 - 09:30:02 PST
