[gmx-users] Freezing a portion of a protein during simulation

Anirban Ghosh reach.anirban.ghosh at gmail.com
Fri Apr 23 13:38:47 CEST 2010


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.


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