Hello everyone;I have posted a question earlier about REMD simulation but i got 
no answer so i am going to re-post it with  ore detail hoping someone might 
give me a hint.  My research focuses on detection and modeling of internal 
dynamics within proteins. My first attempts with gromacs focused on running 
normal md simulation with the addition of residual dipolar coupling data for 
the dynamics from NMR spectroscopy as an orientation restraint itp file added 
to all steps of the simulation ( energy minimization, nvt equiliberation, npt 
equiliberartion and md production) with the hopes that gromacs will be able to 
generate the right trajectory for the dynamics; as a result gromacs was able to 
detect the position of dynamics but failed in simulation the right trajectory, 
not to mention that some secondary structure information were lost. So the same 
procedure was repeated with the addition of dihedral restraint however the 
improvement was minor. So i read in some literature that some groups where able 
to identify and model 4 step dynamics by running REMD with distance restraint 
data, so i thought ill try that but with RDC data instead.My REMD simulation 
has 4  exact replicas each equiliberated in different temperature as in this 
tutorialAn introduction to replica exchange simulations: Mark Abraham, Session 
1B - Gromacs, how ever i did npt equiliberation following the nvt part ( with 
all having the same pressure value).as a result i have 4 (log, edr,xtc) files 
for each replica, but when i try to visualized the trajectory for each replica 
not only do they differ from each other, i notice that in all of them the 
structure of the  protein breaks, some bonds are so stretched that they leave 
the boundary of the box, but the value of the orientation RMSD is always within 
the error range ( the error added to the RDC data) indicating that the 
simulation is applying the rdc data correctly?Can someone explain to me why is 
this happening? or am i suppose to combine the 4 trajectories to view them 
together?I really appreciate any help or any extra tutorial that might help. 
Also if further details of the simulation needed please ask and ill 
ansewr.Thank youHanin Omar

| 
| 
|  | 
An introduction to replica exchange simulations: Mark Abraham, Session 1...


 |

 |

 |



-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Reply via email to