<br><br><div class="gmail_quote">On Sun, May 16, 2010 at 5:15 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;">
<div class="im"><br>
<br>
Amit Choubey wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Justin,<br>
<br>
Since the density (1 gm/cc) and T (300 K) correspond to ambient condition, should not the equation of state dictate a pressure around 1 atm?<br>
<br>
</blockquote>
<br></div>
If the equation of state involves temperature and pressure, yes. </blockquote><div><br>So if you fix the density and temperature shouldnt you land up with right pressure which we know should be 1 atm. <br> </div>amit<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
thank you<br>
amit<div><div></div><div class="h5"><br>
<br>
On Sun, May 16, 2010 at 2:07 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Amit Choubey wrote:<br>
<br>
Hi Everyone,<br>
<br>
I was doing MD with SPC waters and found something which i am<br>
not sure how to explain.<br>
<br>
I made a box of SPC water of dimension 4x4x4 nm^3 and filled<br>
with water using grenbox .<br>
<br>
I then did a nvt simulation at 300 K for 1 ns . I used berendsen<br>
coupling and Reaction - Field for coulomb interaction. Cut off<br>
were all set to 1 nm. Temperature did converge to 300 K. After<br>
this i turned of nvt and did nve with RF-zero for another ns.<br>
Energy was well converged during this (RMSD < 0.1 %).<br>
Temperature was also around 304 K (RMSD < 1%). But the pressure<br>
was 1.1 Kilobar with a fluctuation of 20 % . I don understand<br>
this, shouldnt this be around 1 bar ? Could some one suggest<br>
whats on ?<br>
<br>
<br>
Since an NVE ensemble employs neither a thermostat nor a barostat, I<br>
don't know why you'd expect that.<br>
<br>
-Justin<br>
<br>
Thank you,<br>
amit<br>
<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></div></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><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></blockquote><div><div></div><div class="h5">
<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>
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