Not sure without actually seeing your data, but I suspect you’re choosing a
bandwidth that’s too big, leading to underfit data. What is the bandwidth
that cpptraj chooses for each (via the normal distribution approximation)?
-Dan
On Fri, Aug 31, 2018 at 11:24 PM Mac Kevin Braza <mebraza.up.edu.ph> wrote:
> Hello,
>
> I recently had RMSD values of my protein and use the data from cpptraj to
> do KDE analysis )also in cpptraj). However, I am getting values greater
> than one at specific bandwidth. Is there any way I can avoid getting
> probability values > 1 at fixed bandwidth.
>
> This is how my cpptraj input file look like:
>
> readdata sotyr_apo_EL1_rmsd.dat name EL1
> readdata sotyr_apo_EL3_rmsd.dat name EL3
> readdata sotyr_apo_IL3_rmsd.dat name IL3
> readdata sotyr_apo_IL4_rmsd.dat name IL4
>
> kde EL1 out SoTyrR_EL1_kde.out min 0 max 10 step 0.01 bandwidth 1
> kde EL3 out SoTyrR_EL3_kde.out min 0 max 10 step 0.01 bandwidth 1
> kde IL3 out SoTyrR_IL3_kde.out min 0 max 10 step 0.01 bandwidth 1
> kde IL4 out SoTyrR_IL4_kde.out min 0 max 10 step 0.01 bandwidth 1
>
> run
> quit
>
> Thank you very much!
>
> Best regards,
> Mac Kevin E. Braza
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Received on Sat Sep 01 2018 - 06:00:03 PDT
