[gmx-users] Positive potential energies for Dimethyl Aniline and Aniline
debayan.ch at gmail.com
Mon May 7 05:11:28 CEST 2012
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
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
>> my topolgy files by closely following that given for 2-chloroaniline in
>> molecule and liquids database of virualchemistry.org
>> <http://virualchemistry.org>. I have even downloaded the files of
>> and ran short simulations. In those simulations I get negative potential
>> total energies, and even the Coulomb-recip term is negative.
>> When I switch to my systems aniline and DMA, for both I get negative
>> 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
>> 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
> Does a positive Coulomb recip term indicate
>> 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.
> 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 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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