[gmx-users] Freezing secondary structure

[Justin A. Lemkul]

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 
suitable.

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

http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints

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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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