Sorry for the delay replying!
Yes, by default the ‘grid’ action just increments a voxel every time a
selected atom falls within that voxel. So you have it correct!
-Dan
On Thu, Dec 26, 2024 at 3:47 PM Cianna Calia via AMBER <amber.ambermd.org>
wrote:
> Dear Amber community,
>
> I have been using the following cpptraj input to obtain dx files for
> visualizing the spatial distribution of water around a protein:
>
> parm ../../production/100ns_1/FFFF_TTr1.prmtop
> trajin ../../production/100ns_1/FFFF_TTr1_100ns_1.nc
> autoimage anchor :27-29,47-49,67-69,87-89.CA,C,O,N origin
> principal :27-29,47-49,67-69,87-89.CA,C,O,N dorotation
> rms first :27-29,47-49,67-69,87-89.CA,C,O,N
> average avg.pdb :1-120
> grid FFFF_TTr1_100ns_1_242K_sdfOw-v1.dx 24 0.5 40 0.5 54 0.5 (:WAT.O)
> run
>
> Just want to check if I'm understanding the output correctly: The number
> for each voxel is the number of frames in which that voxel was occupied by
> a water oxygen, right?
>
> Thanks!
> Cianna
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Received on Sat Jan 04 2025 - 10:00:02 PST
