Hi Xing,
Instead of specifying a single number for the water box buffer, you can
instead pass a list (in curly braces) of the buffers in the x, y, and z
directions.
For example
solvatebox UNIT TIP3PBOX {10.0 10.0 5.0}
Will create a box that extends twice as far from the unit in the x
direction as in the y and z.
Generally:
solvatebox UNIT TIP3PBOX {x y z} [closeness]
Hope this helps,
Robin
On Mon, Sep 11, 2017 at 4:27 PM, Xing <stecue.gmail.com> wrote:
> Dear all,
>
> I'm doing some steered MD calculations and the waterbox become elongated
> in the x and y direction, and the solute will "touch" each other
> eventually. I'm thinking to increase the initial length and
> width of the box (but not the height) to avoid the situation. Can we do
> this in xleap? The "solvatebox" command I used only supports a "closeness"
> parameter and it will increase the size of the box in
> all 3 dimensions.
>
> --
> Sincerely yours
> Xing
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Sep 11 2017 - 17:00:02 PDT
