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

[Justin A. Lemkul]

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

-- 
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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

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