To whom it may concern,
I have some issues with centering the protein structure in my simulation
box. The protein is hexameric and my box is a truncated octahedron.
During 1 microsecond of the simulation, protein wonders out of the box.
After the simulation, I calculated the RMSD and it looks like this:
Then I used autoimage from cpptraj, and after RMSD calculation I got
something like this:
I tried various different combinations, with anchoring to the origin,
with anchoring all the amino acids, and the result is the same. I also
tried centering on different structures, and the results are the same.
Do you have any suggestions on how to fix this problem or is this
something that already occurred as a problem?
Thank you in advance for your answer,
--
Boris Gomaz
Laboratory for chemical and biological crystallography
Division of Physical Chemistry
Ruđer Bošković Institute
Bijenička cesta 54, 10000 Zagreb
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Received on Wed Apr 06 2022 - 07:00:03 PDT
