Hi,
So when you direct multiple 1D sets to gnuplot output, cpptraj assumes
you want to make a heatmap-style (pm3d) plot. Because of the way pm3d
works, it looks better if there is an extra row of data (you can check
the difference by deleting the "zero set" and replotting). You can
turn this behavior off by specifying the 'nopm3d' keyword. See the
manual for more details, or type 'help Formats writedata gnu' for
gnuplot-related keywords.
Hope this helps,
-Dan
On Wed, Aug 4, 2021 at 7:36 PM Matthew Guberman-Pfeffer
<matthew.guberman-pfeffer.uconn.edu> wrote:
>
> Dear Amber Community,
>
> I am confused over why the self-correlation of the motion vectors for a residue appears to come out as zero using the below command in cpptraj:
>
> atomiccorr :262,562,553 out acorr.gnu byres
>
> The gnu output I get gives (where I’ve bolded the relevant lines that have me confused):
>
> 1.000 1.000 0.0000
> 1.000 2.000 -0.0299
> 1.000 3.000 -0.0257
> 1.000 4.000 0
>
> 2.000 1.000 -0.0299
> 2.000 2.000 0.0000
> 2.000 3.000 -0.0173
> 2.000 4.000. 0
>
> 3.000 1.000 -0.0257
> 3.000 2.000 -0.0173
> 3.000 3.000 0.0000
> 3.000 4.000 0
>
> 4.000 1.000 0
> 4.000 2.000 0
> 4.000 3.000 0
> 4.000 4.000 0
>
> Best,
> Matthew
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Received on Thu Aug 05 2021 - 11:30:02 PDT
