[gmx-users] loop movement X simulation time

Josmar R. da Rocha bije_br at yahoo.com.br
Wed Oct 22 03:41:27 CEST 2008

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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