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

Justin A. Lemkul jalemkul at vt.edu
Mon May 7 14:33:36 CEST 2012

On 5/6/12 11:11 PM, Debayan Chakraborty wrote:
> 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.

If you are trying to reproduce the results of others, perhaps you should contact 
the authors.  Note that various energetic terms as you've selected are not 
necessarily relevant in the parameterization scheme, and other observables may 
be important as well.


> Best,
> Debayan
> On Mon, May 7, 2012 at 12:31 AM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto: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>
>         <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 <http://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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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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