[gmx-users] secondary structure element constraining

alex rayevsky rayevsky85 at gmail.com
Tue Jun 12 17:23:48 CEST 2018

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


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*

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