[gmx-users] how many dihedral angles should be included for the naphthalene molecule if I use oplsaa

[Ming Han]

 1__2   6__
//     3\/     \\
|        ||4    |
\\___ /\___//
   5  7


I want to know if 1-2-3-6 torsion should be included?
And if both 2-3-4-7 and 6-3-4-5 should be included?
Thanks.

Ming

On Tue, Apr 27, 2010 at 6:43 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Ming Han wrote:
>>
>> Dear all,
>>
>> I want to test a MD simulation job for the naphthalene molecule by the
>> oplsaa force field by. The x2top generated less number of dihedral
>> angles than what I expected. Do you know how many dihedral angles
>> should be included for the naphthalene molecule if I use oplsaa?
>
> It would be helpful to see the [dihedrals] directive that x2top produced, as
> well as an explanation of what you think you should've gotten.  Just saying
> you got less than what you thought isn't very informative.  You may also
> want to consult the primary literature for OPLS to see the derivation of
> bonded parameters and how they might be applied to naphthalene.
>
> -Justin
>
>>
>> Thanks a lot.
>>
>> Ming
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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