[gmx-users] Improper Dihedrals

[Justin A. Lemkul]

Darrell Koskinen wrote:
> 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.
> 

There is still a force constant associated with the improper, so deviations from 
absolute planarity are possible.  Vibrations aren't unexpected, but any severe 
distortions would be problematic.

-Justin

> 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
> 
> 
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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