Dear Justin:<br><br>I finally figure out that the problem comes from the Coulomb 1-4 interactions defined by [pairs] part. When I remove this parts, the energy minimization ends with a big negative number. Thanks for your help.<br>
<br><div class="gmail_quote">On Tue, Jan 26, 2010 at 4:24 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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Yanmei Song wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Justin:<br>
<br><div class="im">
Sorry, that itp is the original one generated by PRODRG. Also I have modified it based on a optimized force field of the molecule. (See attached file and the literature of the force field). But still the potential energy is positively 1e2 and why the system can run well and I can get the reasonable density? Except charge, can you see any obvious mistakes of the itp file? since even if the parameter is not so optimized, I should not get such a big positive potential energy.<br>
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</div></blockquote>
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If you have 27800 molecules, that means you have almost 56000 -OH groups and even more potential H-bond acceptors with the ether oxygens. If there are a lot of unoccupied hydrogen bonding groups, then you have a lot of electrostatic interactions that are unsatisfied. The same situation can occur with, for example, a protein in vacuum. I'm assuming this is the case, but you haven't said whether or not there's solvent.<br>
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As for whether or not you can lump the hydrogen charges into the carbon atoms, that can be debated. The parameter set you've used has no direct relevance to the Gromos parameter set from which you're (presumably) taking atom types. But if you're able to produce a substantial amount of experimental observables, you may be able to justify your methods.<br>
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<br>
-Justin</font><div><div></div><div class="h5"><br>
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<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.vt.edu/Pages/Personal/justin</a><br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Yanmei Song<br>Ph.D. Candidate<br>Department of Chemical Engineering<br>Arizona State University<br>