motion. I don't know whether you removed a ligand and this is a
> functional relaxation, or that is was started from a crystal structure, but
> it is something to be aware of.
>
> Hope it helps,
>
> Tsjerk
>
> On Fri, Dec 18, 2015 at 8:51 PM, Nithyanan Annamalai <
> n
rajectory? Did you cluster and/or make
> everything whole?
>
> By the way, 50 ns is probably too short for a protein of that size. It will
> probably still be relaxing and the eigenvectors will be those of the
> relaxation.
>
> Cheers,
>
> Tsjerk
>
> On Fr
Dear GROMACS users,
I have performed 50ns MD for 567 aa monomer protein using gromos53a6 ff in
explicit water in the cubic box with 2fs time step.
I have used g_covar and g_anaeig to perform Principal Component Analysis/
Essential Dynamics analysis.
But when I view the animation of the traject
