[gmx-users] Freezing secondary structure

seunghwan lee seung43210 at yahoo.com
Tue Sep 6 20:14:52 CEST 2011

Hi All,

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?


Seunghwan Lee

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