[AMBER] problems in using autoimage

From: Giulia Sormani via AMBER <amber.ambermd.org>
Date: Wed, 21 Sep 2022 18:04:04 +0200

Good evening to all,
I am running a NVT simulation of Zr(4+) ion and 4 CL(-1, added to
neutralize the charge) in a cuboid box of water.
I then use the "autoimage" command of cpptraj to visualize the traj
By default, the Zr (first atom of the topology) is blocked in the center
of the box and all the other atoms should be imaged freely.
However, the water box doesn't maintain the cuboid shape, it is deformed,
for examples some voids are created at the edges of the box.
What should I do to visualize the traj correctly?
I did some trials changing the "fixed" and "mobile" masks, but with no

Hope someone can help,


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Received on Wed Sep 21 2022 - 09:30:03 PDT
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