<br><br>in your mail:<br><br><div class="gmail_quote">On 30 March 2011 15:30, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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<br>
Elisabeth wrote:<br>
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Dear all,<br>
<br>
I intend to obtain vaporization heat per volume for a /pure alkane system/. Here is the steps I am taking. Please correct me.<br>
<br>
1- Obtain total energy of system (kinetic+potential) and divide by number of molecules to obtain energy per mol of molecules. g_energy -f *.edr -nmol XXX<br>
2- Obtain total energy of a single molecule (use pbc).<br>
3- Subtract step 2 from step 1.<br>
4- Divide by simulation box volume.<br>
<br>
My questions is:<br>
<br>
in step 2 : what should be the box size? The same size as in 1 or it does not matter? (step 1 is done for the actual denstiy)<br>
<br>
</blockquote>
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More troubling, how does one define the energy of a molecule? If you use any sort of long-range algorithms (especially PME, but also dispersion correction), you can't simply decompose the system like this.<br>
<br></blockquote><div>Thanks Justin and David.<br>
<br>
I have been trying to find the article in which this has been presented.
If you have time Please see page 5937, right column, equation 11. I think I made a mistake and I dont have to include kinetic energy, Only nonboded energies!?<br>
<br>
<a href="http://pubs.acs.org/doi/pdfplus/10.1021/jp0707539">http://pubs.acs.org/doi/pdfplus/10.1021/jp0707539</a><br><br> </div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
In the derivation of recent Gromos96 parameter sets, the heat of vaporization is quite simple:<br>
<br>
DHvap = <Ugas> - <Uliq> + RT<br></blockquote><div><br>1- So <Uliq> is the total energy or only potential (no kinetic)<br>2- How can I compute <Ugas>? I have liquid now...<br></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Thank you,<br>
Regards,<br>
<br>
</blockquote>
<br>
-- <br>
========================================<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.vt.edu/Pages/Personal/justin</a><br>
<br>
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