Ok, The protein I am going to simulate is from a hyperthermophilic organism<br>which lives in deep oceanic thermal vents. so in the deep vents the pressure<br>will be enormous. even though I do not have much information about the<br>
magnitude of pressure in that site and inside the cell of that organism.. I may <br>be able to get some rough estimate of pressure..<br><br>So I wanted to simulate this protein at a temperature near 90 or 100 deg C.<br><br>
Thank you<br>With Regards<br>Kavya<br><br><div class="gmail_quote">On Mon, Oct 17, 2011 at 8:45 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="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im"><br>
<br>
Kavyashree M wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hello,<br>
<br>
I am sorry those were two different questions.. I wanted to know what<br>
this statement actually mean?<br>
"The set pressure should reflect whatever system you are trying to model."<br>
<br>
</blockquote>
<br></div>
You haven't fully explained what exactly you're trying to do yet, so I'm taking a stab in the dark. Let's say you're trying to simulate a benchtop experiment with a protein in solution over a heating mantle at 350 K. The pressure is 1 atm under such circumstances (NPT). Now let's say you want to simulate the behavior of a protein solution in a bomb calorimeter (constant volume) at 350 K. The pressure is not likely to be 1 atm under such circumstances (but then too, you'd use NVT instead of NPT, but maybe after NPT equilibration at whatever the necessary pressure is). Without a fully detailed description of what you'd like to accomplish, I'm going to stop guessing.<br>
<br>
You've asked a lot of scattered questions about different topics, which makes it less efficient for people to help you and less clear for you to understand what we're trying to communicate back, even if it is somewhat generic.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
Thank you<br>
With Regards<br>
Kavya<br>
<br>
<br>
I don't see the connection to my comment about pressure, but I'll<br>
address this anyway. There is no temperature during EM. Hence with<br>
"gen-vel = no" then no velocities are generated. The settings for<br>
gen-temp and gen-seed are defaults that are assigned when none are<br>
provided in the input .mdp file.<br>
<br>
I seem to recall that a pressure term is written during EM, but it<br>
is largely meaningless.<br>
<br>
-Justin<br>
<br>
<br></div>
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Justin A. Lemkul<br>
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ICTAS Doctoral Scholar<br>
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Virginia Tech<br>
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Justin A. Lemkul<br>
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Department of Biochemistry<br>
Virginia Tech<br>
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