[gmx-users] secondary structure element constraining

[alex rayevsky]

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??

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


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 ?

Thank You!





*Nemo me impune lacessit*