[gmx-users] Improper Dihedrals

[Tsjerk Wassenaar]

Hi,

If you turn all bonds to constraints, and your system is infinitely
periodic, you probably don't even need impropers. The bond lengths can
only be satisfied in the plane. Adding impropers, straining your
molecule further into the configuration you think is proper, adds
forces that inevitable come with vibrations. The higher the straining
(the forces), the higher the frequencies, the smaller you have to set
your time step to be sure not to get into trouble. Then again,
everything moves and surely graphene sheets vibrate. The big question
here is: what is the out of plane vibration of atoms in a graphene
sheet? Googling "graphene out plane vibration" gives the following for
a  first hit: http://www.iop.org/EJ/article/0370-1301/69/12/319/prbv69i12p1326.pdf
Maybe that's a good start to get your system tuned?

Cheers,

Tsjerk

On Tue, Aug 11, 2009 at 9:41 PM, Justin A. Lemkul<jalemkul at vt.edu> wrote:
>
>
> 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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>
> --
> ========================================
>
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623