[gmx-users] Freezing secondary structure

Justin A. Lemkul jalemkul at vt.edu
Tue Sep 6 20:17:49 CEST 2011

seunghwan lee wrote:
> 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. 

Angle restraints wouldn't fix secondary structure; dihedral restraints are more 

> What is the best way to freeze the secondary structure (a-helix in my case) during simulations?


I suppose an alternate would be to have genrestr generate a distance restraint 
file for you, but complex distance restraints limit performance because there 
are difficulties parallelizing such systems.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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