[gmx-users] Improper Dihedrals

[Darrell Koskinen]

Dear GROMACS Gurus,
I assigned improper dihedrals to my graphene structuure but still see it 
vibrating. Is this to be expected? I thought the purpose of improper 
dihedrals was to keep planar structures planar.

Here is a copy of a couple of sections of my topology file after 
assigning the improper dihedrals to my graphene structure:

#define improper_dihedral improper_Z_CA_X_Y

[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1            
c2            c3            c4            c5
    3     1     2     5     1    improper_dihedral
    2     1     3     7     1    improper_dihedral
    2     1     4     9     1    improper_dihedral
    1     2     5    11     1    improper_dihedral
    1     2     6    13     1    improper_dihedral