I think PCA could be helpful depending on the motions in your system. I
would suggest that you carry out a single PCA analysis on the full
trajectory data including all temperatures though. If you do pca separately
it is difficult to compare them. Then you can project each temperature
separately, using the same vectors.
See this tutorial:
https://amberhub.chpc.utah.edu/introduction-to-principal-component-analysis/
On Mon, Aug 12, 2024, 5:52 PM ABDELATIF MESSAOUDI <amessaoudi.univ-batna.dz>
wrote:
> Dear Prof Carlos
> Thank you for your response.
>
> I am specifically looking to understand how temperature affects the
> conformational dynamics of my system. By performing PCA at different
> temperatures, I hope to identify any significant changes in the principal
> components that could indicate temperature-dependent structural variations.
>
> Could you please provide guidance on whether my current approach is
> suitable for this analysis, or if there are additional steps or
> considerations I should take into account?
>
> Thank you for your help.
>
> Best regards,
>
> Abdelatif
>
> Le lun. 12 août 2024 à 23:29, Carlos Simmerling <
> carlos.simmerling.gmail.com> a écrit :
>
>> It will help if you can share what information you want to learn,
>> otherwise we can only direct you to the manual and tutorials. What is it
>> about your data that you want to understand using PCA at different
>> temperatures?
>>
>> On Mon, Aug 12, 2024, 2:37 PM ABDELATIF MESSAOUDI via AMBER <
>> amber.ambermd.org> wrote:
>>
>>> Dear AMBER Users,
>>>
>>>
>>>
>>> To address a question from a reviewer regarding Principal Component
>>> Analysis (PCA) at different temperatures, I followed the tutorial
>>> available
>>> at the following link:
>>>
>>> https://ambermd.org/tutorials/advanced/tutorial41/
>>>
>>> I have attached my input file, Python script, and the resulting image for
>>> your reference.
>>>
>>>
>>>
>>> Could you please advise if this approach is correct, or if there is
>>> anything else I should consider?
>>>
>>>
>>>
>>> Thank you for your assistance.
>>>
>>>
>>>
>>> Best regards,
>>>
>>>
>>>
>>> Abdelatif Messaoudi
>>>
>>> University of Batna 1,Algeria
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
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Received on Mon Aug 12 2024 - 15:30:02 PDT
