On Wed, Apr 04, 2018, M Conte wrote:
> I'm trying to create a slab of water in Amber14, and I'm looking to
> increase the z-dimensions of a box of water after a production run to
> create the slab-like shape. I know that it's possible to alter the three
> parameters at the end of restart files to create a new box, but it looks
> like one can only increase or decrease box dimensions in the positive
> direction. Is there an alternative way to increase the box length along the
> negative z axis in addition to the positive, so that the slab is enveloped
> by two layers of empty space?
Amber's box origin is (by default) always at (0,0,0). But remember that
you are dealing with periodic systems: if you add empty space by
increasing the z-dimension, you are also adding empty space to its
periodic image (e.g. along the negative z-axis).
...good luck....dac
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Received on Thu Apr 05 2018 - 08:00:03 PDT
