> both oct or cubic should be fine, especially for your simple system, as long as they are equilibriated later.
...
> solvatebox aba TIP3PBOX 12.0
> Solute vdw bounding box: 77.859 58.790 54.861
...
I would suggest they are not equal. Yes, equilibration is important. If
you have a solute that is longer in a particular dimension, it will rotate
during MD unless you prevent this. Rotation occurs rapidly, usually on a
nanosecond time scale. This could bring images closer together. In your
particular case since the truncated octahedron required more waters to
solvate suggests a solute that is longer in one dimension. I would run
with the box that is closer to spherical, i.e. use solvateoct.
--tec3
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Received on Sun Oct 09 2011 - 18:00:03 PDT
