AMBER Archive (2006)

Subject: AMBER: Fully QM periodic runs

From: Steven Winfield (
Date: Wed Jun 14 2006 - 11:03:43 CDT

Dear Amber users,

I am trying to perform a QM/MM run on a box of water, treating
everything quantum mechanically, but I'm running into some problems.
If I use, for example, the TIP3PBOX unit as my input structure then
sander fails because the size of the QM region is bigger than the
periodic box. This is due to some atoms protruding out of the primary
simulation cell. Even if I turn on iwrap=1 the problem is still present
because the wrapping is done to the whole molecule only when the first
atom of that molecule moves out of the primary cell. Also, introducing
some vacuum around the structure still fails when molecules cross the
new cell boundary.

So my question is: Can a fully QM periodic run be done in the current
AMBER, and if so how? (Wrapping atoms back into the primary cell
individually rather than with the rest of the molecule for example?)


Steve Winfield.
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