[gmx-users] how many dihedral angles should be included for the naphthalene molecule if I use oplsaa
Justin A. Lemkul
jalemkul at vt.edu
Wed Apr 28 02:43:43 CEST 2010
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?
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
You can also look into the literature. A simple Google search for "napthalene
OPLS" (without the quotes) turns up tons of simulation papers.
> 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.
>>> Thanks a lot.
>> 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
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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