Yes. Both are correct, it is just a matter of perception or interpretation. The system is periodic; in many molecular graphics programs (like Chimera or VMD) you can visualize the neighboring periodic images and see that both "interpretations" are equivalent.
You can also try to "image" using CPPTRAJ and the autoimage command...
With iwrap=0 it will appear that the solvent is diffusing away, however realistically (assuming constant pressure and no artifacts leading to vacuum bubbles) the solvent is just moving into a nearby periodic image (i.e. effectively crossing the box edge back into the other side if wrapped)...
--tec3
________________________________________
From: Lucas Bandeira <bandeiralucas97.gmail.com>
Sent: Wednesday, June 26, 2019 12:26:26 PM
To: AMBER Mailing List
Subject: [AMBER] Problems with iwrap
Dear AMBER Community,
I was performing simulations of a Gold-Water interface to study electric
Double Layer. I've notice that when I use the flag iwrap = 1, the gold
atoms in the slab leave the well-organized structure, what it's not
supposed to happen, but the calculations are performed normally. I've set
iwrap = 0 and the problem stopped. Could somebody helps me explaining why
that happens?
Sincerely yours,
Lucas Bandeira
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 26 2019 - 16:30:02 PDT
