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

[Justin A. Lemkul]

Ming Han wrote:
>  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.
> 

I would think that proper dihedrals would not even be used for such a molecule. 
  The fused ring systems will utilize impropers to stay planar.  For example, 
the TRP side chain specifies no proper dihedrals within the indole side chain; 
only impropers are used, but maybe someone with more OPLS derivation experience 
can comment.

You can also look into the literature.  A simple Google search for "napthalene 
OPLS" (without the quotes) turns up tons of simulation papers.

-Justin

> 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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> 

-- 
========================================

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

========================================