[gmx-users] secondary structure element constraining

[Justin Lemkul]

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The webpage is outdated; kfac is now just k, the actual force constant.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That link is also outdated.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

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

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