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The webpage is outdated; kfac is now just k, the actual force constant.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That link is also outdated.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.
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Virginia Tech Department of Biochemistry

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