Hi all,
I have several sets of MD runs and I would like to perform PCA analysis using Amber.
I am quite a newbie with this package being mostly used to Gromacs/NAMD.
In particular I would need to calculate:
1- The histogram of the first 5 eigenvalues
2- Dot product of the essential deformation modes taking into consideration the first 10 eigenvalues (which should describe the ~90% of the driving motion).
Do you know which chain of commands put together to achieve the goal?
Thanks in advance to anyone for you kind help.
Regards
VG
https://amberhub.chpc.utah.edu/introduction-to-principal-component-analysis/
Thank you.
I have pretty much done everything.
However, I would like to obtain a table of the Overlap values for the eigenvectors, as reported in Table II by Skjaerven, L. et all., Proteins (Article Principal component and normal mode analysis of proteins; a ...
)where PC1 (of MD1) is put vs PC1, PC2 and PC3 (of MD2) and so on...
Have you ever realized a table like that one?
If so, which Amber output do you take into account to realize it?
Thanks in advance to all of you.
Alexander Jussupow
Aashish BhattVito
Alexander Jussupow
, thank you for the recommendation. I wonder whether these python modules work with MD runs performed using other softwares like YASARA.
Aashish Bhatt, thank you for the recommendation. I wonder whether it works with MD runs performed using other softwares e.g. YASARA.
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