[gmx-users] loop movement X simulation time

Justin A. Lemkul jalemkul at vt.edu
Wed Oct 22 04:41:19 CEST 2008

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?

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.


> 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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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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