Yes, that tutorial can help you compare two trajectories if they have
a 1:1 correspondence. Let me know if you have any questions regarding
the tutorial or if it can be improved.
Best,
Rodrigo.
On Wed, Jan 19, 2022 at 2:30 PM Reza Khayat <rkhayat.ccny.cuny.edu> wrote:
>
> Hi,
>
> Thanks. Is this the tutorial?
>
> https://amberhub.chpc.utah.edu/introduction-to-principal-component-analysis/
>
> Best wishes,
> Reza
>
> Reza Khayat, PhD
> Associate Professor
> City College of New York
> Department of Chemistry and Biochemistry
> New York, NY 10031
>
> ________________________________________
> From: Thomas Cheatham <tec3.utah.edu>
> Sent: Wednesday, January 19, 2022 4:16 PM
> To: AMBER Mailing List
> Subject: [EXTERNAL] Re: [AMBER] Comparing trajectories
>
> As long as you have a 1:1 mapping among the atoms selected for the PCA; you want to do "combined PCA" so that the modes are equivalent in each (i.e. combine trajectories and separately project on each trajectory). I think there is a tutorial on amberhub.chpc.utah.edu but that site is hanging at the moment (I alerted the team).
>
> --tec3
>
> ________________________________________
> From: Reza Khayat <rkhayat.ccny.cuny.edu>
> Sent: Wednesday, January 19, 2022 2:04 PM
> To: AMBER Mailing List
> Subject: [AMBER] Comparing trajectories
>
> Hi,
>
>
> I have a naïve question. Is it possible to compare the conformational states that a protein complex can adopt under two different conditions? If I have a trajectory for each condition, can I do PCA for each condition and compare the PCA results? Thanks.
>
> Best wishes,
>
> Reza
>
>
> Reza Khayat, PhD
> Associate Professor
> City College of New York
> Department of Chemistry and Biochemistry
> New York, NY 10031
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Received on Wed Jan 19 2022 - 14:00:03 PST
