Dear Justin,<br> 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. <br>
<br>Best,<br>Debayan<br><br><div class="gmail_quote">On Mon, May 7, 2012 at 12:31 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im"><br>
<br>
On 5/6/12 11:42 AM, Debayan Chakraborty wrote:<br>
</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
Dear Colleagues,<br>
I am trying to build a well equilibrated solvent box<br>
of aniline and N,N dimethyl aniline using the OPLS-AA parameters. I have built<br>
my topolgy files by closely following that given for 2-chloroaniline in the<br>
molecule and liquids database of <a href="http://virualchemistry.org" target="_blank">virualchemistry.org</a><br></div>
<<a href="http://virualchemistry.org" target="_blank">http://virualchemistry.org</a>>. I have even downloaded the files of chloroaniline<div class="im"><br>
and ran short simulations. In those simulations I get negative potential and<br>
total energies, and even the Coulomb-recip term is negative.<br>
<br>
When I switch to my systems aniline and DMA, for both I get negative potential<br>
energies for the minimized structure. However, the coulomb-recip term is<br>
positive in both cases. When I start my MD total energies for both aniline and<br>
DMA become positive, though aniline still retains a negative value of potential<br>
energy, the potential for DMA becomes positive.<br>
<br>
My questions are : Are positive or negative energies of a system during<br>
simulation real indicators of something wrong in your MD ?<br>
</div></blockquote>
<br>
A positive potential indicates net repulsion. In a normal, condensed-phase system, there should be net attraction.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
How is it possible that chloroaniline, aniline and<br>
DMA which are closely related systems have so different values of energies ?<br>
</blockquote>
<br></div>
"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.<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Does a positive Coulomb recip term indicate wrong<br>
representation of electrostatics ?<br>
<br>
</blockquote>
<br></div>
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.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
For all the systems I have used the charges from the OPLS-AA force field. Any<br>
</blockquote>
<br></div>
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.<br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
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