Justin A. Lemkul wrote:
Josmar R. da Rocha wrote:
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?
Maybe; it is hard to say for sure.
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).
Protein motions are difficult to predict. Some may oscillate very
quickly (within a few ns), others may be very slow (tens/hundreds of ns
or more).
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?
Or you can try a higher T.
Never say never :) Realize that simulations are random, so you may have
to run several different simulations, starting from different initial
velocities, to get better conformational/statistical sampling. Normal
modes analysis may also be appropriate for your system, depending on the
degree of conformational flexibility of your protein.
-Justin
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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________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
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