[gmx-users] Dihedral between non bonded atoms

Momin Ahmad momin.ahmad at kit.edu
Thu Jul 12 12:01:37 CEST 2018


is there a reason why gromacs demands parameters for dihedral angles 
that are not bonded? For example i,j, and k are bonded but l is not. The 
distance of k and l is about 2.7 Angstroem. How can i tell gromacs to 
ignore these dihedrals during pdb2gmx. I did no define a bond in the 
.rtp file. The .pdb i used for pdb2gmx is attached.
Thanks in advance.


Momin Ahmad

Karlsruhe Institute of Technology (KIT)
Steinbuch Centre for Computing (SCC)
Hermann-von-Helmholtz-Platz 1
76344 Eggenstein-Leopoldshafen
Phone: +49 721 608-24286
E-Mail: Momin.Ahmad at kit.edu

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