[gmx-users] Topology file

Aranha, Michelle maranha at vols.utk.edu
Fri Jan 2 21:32:25 CET 2015


I wanted to create a topology file without the bonds, angles and dihedrals for a CNT fixed in space using position restraints. I use the g_x2top program for building the topology. My understanding was that if I comment out the #include ffbonded.itp in the forcefield.itp file. I should have a topology file without bonds, angles and dihedrals. However, the topology file I get has all bonds, angles and dihedrals. I also tried deleting the ffbonded.itp file from the directory but got the same result. I am not sure how the program works. I understand that I can edit out the bonds, angles and dihedrals lines in topology file, but I would just like to know how does the program generate the topology file even when I don't specify the bonded parameters.

Best regards,


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