Hi Friends,<br>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.<br><br>Cheers,<br><BR><BR><div><font color="#0000bf" size="4"></font> </div> <div style="color: rgb(0, 0, 191);"><strong>Anirban Ghosh</strong></div> <div style="color:
rgb(0, 0, 191);"><strong>M.Tech Bioinformatics</strong></div> <div style="color: rgb(0, 0, 191);"><strong>University of Hyderabad<br></strong></div><span style="font-weight: bold;"><span style="color: rgb(0, 0, 191);">Project Trainee</span><br style="color: rgb(0, 0, 191);"><span style="color: rgb(0, 0, 191);">Centre For DNA Fingerprinting & Diagnostics (CDFD)</span><br style="color: rgb(0, 0, 191);"><span style="color: rgb(0, 0, 191);">Hyderabad</span><br style="color: rgb(0, 0, 191);"><span style="color: rgb(0, 0, 191);">India</span><br></span><p> 
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