Greeting
I'm working on a MD of a ligand-protein complex during 40 ns
i want to analyses ligand-protein interaction hydrogen bonds
My first question :
Should i analyses a minimized frame from clustering of the trajectory
or should i analyses hydrogen bond occupancy over trajectory ?
My second question :
Is it more correct if i do my analysis over the equilibrated phase of MD
(based on RMSD, radius of gyration , etc ...) for example the last 10 ns,
than doing it over the whole trajectory (40 ns) ?.
thanks
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