The origin is the set of coordinates of the lower grid corner. I.e., the most negative point along the x, y and z axes.
To the get the center of box (which may be the center of mass of the solute, depending on your choice of `centering`), multiply the number of grid points by the delta and add it to your origin. E.g., in your case the center of the box along the x-axis is
-18.08241552 + 240 * 0.5 = 101.9175845
Hope this helps,
Tyler
Sent with ProtonMail Secure Email.
‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
On Tuesday, December 28th, 2021 at 5:32 AM, angad sharma <angadsharma54.gmail.com> wrote:
> I am confused about the ORIGIN, which we get in the DX output file after
>
> performing the 3DRISM calculation. Is it the center of mass of the
>
> corresponding PDB structure about which the 3DRISM analysis is going on or
>
> something else?
>
> Here I am pasting a few beginning lines from the DX file:-
>
> object 1 class gridpositions counts 240 240 260
>
> origin -18.08241552 -16.00975162 -13.00657075
>
> delta 0.50000000 0 0
>
> delta 0 0.50000000 0
>
> delta 0 0 0.50000000
>
> object 2 class gridconnections counts 240 240 260
>
> object 3 class array type double rank 0 items 14976000
>
> data follows
>
> 0.99991E+000 0.10001E+001 0.99991E+000
>
> 0.10001E+001 0.99991E+000 0.10000E+001
>
> 0.99992E+000 0.99997E+000 0.99992E+000
>
> 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 Thu Dec 30 2021 - 11:00:02 PST
