Can anyone help with molecular dynamics -PCA analysis in gromacs?

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Elias Santos

No, there is no criterion for this. Depends on what you want to see in their molecule.

What you wanna see?

Ari Zeida

Hi Nivedita,

I think the best way to check on the convergence of your MD exploration (therefore the relaibility of your PCA analysis) is to calculate the cosine content

Check out this link: http://comments.gmane.org/gmane.science.biology.gromacs.user/55722

Good luck,

Ari