[gmx-users] Protein Moving Out of Box in ED

Anirban Ghosh anirbanz83 at yahoo.co.in
Tue Jan 22 09:39:04 CET 2008

Hi Friends,
I am simulating a 463 aa protein in water only along the 1st Eigen Vector i.e. I am trying to do Essential Dynamics along First Principle Component. I have used the make_edi command to generate a .edi file and then using it to run the mdrun. But my problem is that every time after a simulation of 5 nano second, I am finding that the pretein is coming out ofthe water box, partially. I am using VMD to view the dynamics after the simulation is complete. Is it a problem with GROMACS or VMD or is it that since I am using Periodic Boundary Condition, the portion of the protein which is looking to be outside the box, is actually inside another adjacent box, partally? Is there any way to rectify this or am I doing the correct thing? Please suggest. Any suggestion is welcome. Thanks a lot.


  Anirban Ghosh
  M.Tech Bioinformatics
  University of Hyderabad

Project Trainee
Centre For DNA Fingerprinting & Diagnostics (CDFD)

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