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 <jalem...@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
========================================
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