Hi ALL, I want to do a MD simulation by restraining (freezing) the helical portions and allowing only the loop regions to move. I tried doing this by applying heavy restrain on the helical residues by generating a .itp file with the "genrestr" command with an index file containing the desired residue numbers. However during the simulation I am finding that the entire protein is moving. Am I doing anything wrong? Or is there any other way to freeze a portion of a protein? Any suggestion is welcome. thanks a lot in advance.
Regards, Anirban
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