Dear Gromacs users
I set a 8 ns MD simulation aiming to get a view insight a hypothesized open and
closed state of a protein loop. Many crystallografic structures have been
solved but none of then shows the open state. Besides bfactor for the loop
region to be high, when analysing a partial result (at 2.5 ns) I could not see
any intense conformational change (nor any such open state). I noticed that
there are two HB stabilizing the closed state.
1- Was the time I set too short?
2- How much time should set to make possible these interactions to break to
allow the open state conformation (I've seen in literature times ranging from 2
to 120 ns to study loop movements).
3- Since the time versus protein backbone RMSD plot shows the equilibration of
protein structure after some time is it reasonable to imagine that after that
it is not possible such loop movement to be achieved?
I apologize If my questions sound naive but that's my first MD simulation. I'd
appreciate any help.
Josmar Rocha
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