[gmx-users] Positive potential energies for Dimethyl Aniline and Aniline

[Debayan Chakraborty]

Dear Justin,
                   The Jorgensen group have already published results for
aniline and DMA using the OPLS-AA parameters. I am using the charges from
their publication ( R. Rizzo and W.L.Jorgensen, J.Am.Chem.Soc., 1994, 121,
4827-4836). Even after several crosschecks I have not been able to address
the problem.

Best,
Debayan

On Mon, May 7, 2012 at 12:31 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/6/12 11:42 AM, Debayan Chakraborty wrote:
>
>> Dear Colleagues,
>>                           I am trying to build a well equilibrated
>> solvent box
>> of aniline and N,N dimethyl aniline using the OPLS-AA parameters. I have
>> built
>> my topolgy files by closely following that given for 2-chloroaniline in
>> the
>> molecule and liquids database of virualchemistry.org
>> <http://virualchemistry.org>. I have even downloaded the files of
>> chloroaniline
>>
>> and ran short simulations. In those simulations I get negative potential
>> and
>> total energies, and even the Coulomb-recip term is negative.
>>
>> When I switch to my systems aniline and DMA, for both I get negative
>> potential
>> energies for the minimized structure. However, the coulomb-recip term is
>> positive in both cases. When I start my MD total energies for both
>> aniline and
>> DMA become positive, though aniline still retains a negative value of
>> potential
>> energy, the potential for DMA becomes positive.
>>
>> My questions are : Are positive or negative energies of a system during
>> simulation real indicators of something wrong in your MD ?
>>
>
> A positive potential indicates net repulsion.  In a normal,
> condensed-phase system, there should be net attraction.
>
>
>                              How is it possible that chloroaniline,
>> aniline and
>> DMA which are closely related systems have so different values of
>> energies ?
>>
>
> "Closely related" is in the eye of the beholder.  Even small changes to
> chemical substituents can produce wildly different properties.  Yes, the
> molecules have the same general structure and "shape," but modifications of
> chemical groups can change the very nature of the molecule.  For instance,
> dimethylation of the amine on aniline removes its ability to form hydrogen
> bonds.
>
>
>                              Does a positive Coulomb recip term indicate
>> wrong
>> representation of electrostatics ?
>>
>>
> Again this indicates net repulsion in the long-range electrostatic term
> (from PME).  It probably indicates that your model is not adequate, as the
> molecules are likely to be repelled from one another.
>
>
>  For all the systems I have used the charges from the OPLS-AA force field.
>> Any
>>
>
> How so?  If you're deriving parameters for a new topology, what exactly
> are you using?  Charges are not necessarily transferrable between
> molecules, though many common groups are.  Be careful what you interpret as
> "similar enough" if this is what you're doing.
>
> -Justin
>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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