[gmx-users] loop movement X simulation time

David van der Spoel spoel at xray.bmc.uu.se
Wed Oct 22 08:10:19 CEST 2008

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.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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