[gmx-users] Freezing secondary structure
seung43210 at yahoo.com
Tue Sep 6 20:14:52 CEST 2011
I am trying to run simulations of a small protein with the backbone frozen,
but not the side chains. It looks like neither position restraint run or
defining freeze_group will work since these options will freeze atoms in
space. I also noticed that I may define [dihedral_restraints] and
[distance_restraints], but I couldn't find something like [angle_restraints]. This approach sounds quite tedious as well.
What is the best way to freeze the secondary structure (a-helix in my case) during simulations?
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