Re: [AMBER] problems in using autoimage

From: Daniel Roe via AMBER <>
Date: Wed, 21 Sep 2022 14:49:00 -0400


What version of cpptraj are you using? This sounds like it might be an
older one that doesn’t handle imaging after a unit cell rotation ( from
e.g. rms fit).


On Wed, Sep 21, 2022 at 12:04 PM Giulia Sormani via AMBER <>

> 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
> correctly.
> 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
> success.
> Hope someone can help,
> Giulia
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Received on Wed Sep 21 2022 - 12:00:02 PDT
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