<br><br><div class="gmail_quote">On Mon, May 17, 2010 at 6:45 AM, 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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Amit Choubey wrote:<br>
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On Sun, May 16, 2010 at 7:41 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>
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Amit Choubey wrote:<br>
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On Sun, May 16, 2010 at 5:15 PM, Justin A. Lemkul<br>
<<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>><br></div><div class="im">
<mailto:<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>
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Amit Choubey wrote:<br>
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Hi Justin,<br>
<br>
Since the density (1 gm/cc) and T (300 K) correspond to<br>
ambient<br>
condition, should not the equation of state dictate a<br>
pressure<br>
around 1 atm?<br>
<br>
<br>
If the equation of state involves temperature and pressure, yes.<br>
<br>
So if you fix the density and temperature shouldnt you land up<br>
with right pressure which we know should be 1 atm.<br>
<br>
<br>
You are not fixing (or conserving) the temperature in an NVE<br>
ensemble. That would be an NVT ensemble, employing a thermostat. <br>
<br>
I did do NVT first and then for sampling i removed the thermostat. Also as you mentioned there was not much difference b/n pressure values during NVT or NVE . The pressure value is as high as 1000 bar in both cases.<br>
<br>
<br>
Since instantaneous pressure is calculated (in part) from the<br>
kinetic energy, and since the kinetic energy is not guaranteed to be<br>
conserved, the pressure term will also fluctuate accordingly.<br>
<br>
<br>
This is correct. The pressure thus fluctuates about 20 % of the above mentioned value.<br>
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<br>
<a href="http://www.gromacs.org/Documentation/Terminology/Pressure" target="_blank">http://www.gromacs.org/Documentation/Terminology/Pressure</a><br>
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The internal energy of the system is constant in an NVE ensemble,<br>
the other terms may fluctuate as necessary such that all microstates<br>
occur with the same probability and the energy surface remains flat. <br>
<br>
I agree<br>
<br>
Also recall that an NVE ensemble represents a thermodynamically<br>
isolated system, not conducting heat or engaging in work with the<br>
surrounding system. <br>
<br>
true<br>
<br>
So any concept of external pressure and equilibrating the pressure<br>
is irrelevant.<br>
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<br>
I am not trying to equilibriate the pressure. I am trying to measure the pressure. I also know that at 300 K and 1gm/cc the P should be 1 bar.<br>
<br>
Also, theoretically NVE or NVT are no different than NPT as far as measuring observables is concerned. Hence i was thinking that if you have the right volume density and temperature shouldnt you have the right pressure.<br>
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I think the disconnect is arising because you're expecting a model of water to behave almost like an ideal gas. The SPC water model, under NPT conditions of 300 K and 1 bar, does not give the experimental density of water; it is actually somewhat less than 1 g/mL. So constraining the system to fit some pre-conceived notion of the volume to force the density to be right conflicts with the properties of the water model itself. SPC wants to be at a lower density, you're forcing it to be at a higher density, all while fixing the volume of the simulation cell. Sounds to me like a recipe for high pressure, since SPC wants to expand but you won't let it.<br>
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So the starting configuration, assembled with the right density, has not properly equilibrated under NPT conditions, yet you are expecting it to do so when applying NVE conditions. I don't know that you'll ever be able to satisfy all of these requirements simultaneously unless you can come up with a better water model that replicates both ideal and real behavior :)<br>
</blockquote><div><br>yes model is an issue too. I was just concerned about 3 orders of magnitude of difference in calculation of pressure. Thank you for the answering.<br><br>amit<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<font color="#888888">
<br>
-Justin</font><div><div></div><div class="h5"><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>
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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