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.
Cheers,
Anirban Ghosh
M.Tech Bioinformatics
University of Hyderabad
Project Trainee
Centre For DNA Fingerprinting & Diagnostics (CDFD)
Hyderabad
India
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