[gmx-users] secondary structure element constraining

Justin Lemkul jalemkul at vt.edu
Tue Jun 12 19:42:41 CEST 2018

On 6/12/18 11:23 AM, alex rayevsky wrote:
> Yes, it does... Should I follow this advices
> http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints ?
> Phi/Psi lines are like in the sample, with only changed values of atom
> indexes and angles, measured with pymol of gromacs tools
> ai   aj    ak    al |  type  | label  |   phi          | dphi  kfac  power
>     my atom indices  | 1      |    1   | measured value | 0       1      2
> dphi (seems to be 0 if I want to immobilize this geometry) and kfa (is
> equal to 1 or it means 1000kJmol-1nm-2) as I understood, power label are
> not implemented and type has only one value = 1. Am I right??

The webpage is outdated; kfac is now just k, the actual force constant. 
It's no longer in the .mdp file, at least for a few versions. Check the 
reference manual for whichever version you are using.

> 1. find both phi/psi from the strtucture for each residue
> 2. add to the top file as You corrected here
> https://www.researchgate.net/post/How_can_I_change_and_fix_dihedral_angle_during_Gromacs_simulation_using_dihedral_restraints

That link is also outdated.

> and why are freezing of COM pulling cylinder code (to allow some
> degree of oscilation) less appropriate methods? or simple genrestr
> with 10000 kJ forces ?

I have no idea how the cylinder pull code applies here.

Position restraints might work, but you're imposing different kinds of 
bias there. If you want a constant secondary structure, restrain the 
degrees of freedom that directly define that secondary structure.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


More information about the gromacs.org_gmx-users mailing list