[gmx-users] Updated REMD question

[Hanin Omar]

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

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


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