Hi,
Not fully sure how cpptraj computs KDEs, but my guess is that you are
plotting probability densities, NOT probabilities. Easy to check: If the
integral of your KDE = 1, then you are plotting probability densities,
which could be of course larger than 1, depending on the step you chose.
Adrian
On 9/1/18 8:48 AM, Daniel Roe wrote:
> 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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--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Mon Sep 03 2018 - 07:00:02 PDT
