On Wed, Sep 21, 2022, Giulia Sormani via AMBER wrote:
>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.
It's likely that the initial density of your system does not match what the
force field wants, and that is creating voids in the structure. I'd
continue with NPT simulations until the density is converged, and then re-do
the visualization.
...good luck...dac
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Received on Wed Sep 21 2022 - 18:30:03 PDT
