<br><br><div class="gmail_quote"><span class="Apple-style-span" style="border-collapse: collapse; "><div class="im" style="color: rgb(80, 0, 80); ">On Thu, Apr 9, 2009 at 6:36 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank" style="color: rgb(42, 93, 176); ">jalemkul@vt.edu</a>></span> wrote:<br>
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<div><br><br>Joe Joe wrote:<br><blockquote class="gmail_quote" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex; ">
So I got my small water box (800 waters) to behave stably with pressure coupling after more minimization but I still can't get my large system to work with pressure coupling. I tried minimizing but I can never get the Fmax to be less 10^2, which is pretty normal for protein/water simulations of large proteins, at least from my experience. I have since run 400 ps NVT as the system (425K atoms) is quite stable. The <P.E.> is 2E-05. Since I am using 4fs time steps gromacs won't let me use a tau_p less than .4. Not sure what else to do except run NVT, which is what I was going to do after I got the density equilibrated. BTW, I am using octahedral PBC, but that should not make a difference with respect to P coupling, should it? Below is my whole mdp file. As a reminder my density in the system goes from 1.0 - .1 in 10 ps with Pcoupl = Berendsen and Tau_p = .4. If I increase Tau_P then the amount of time it takes for my system to expand increases but it still expands.<br>
<br></blockquote><br></div>This seems truly bizarre. How are you measuring the density (g_density, g_energy, etc)?</blockquote><div><br></div></div><div>Both g_energy and g_density.<br></div><div class="im" style="color: rgb(80, 0, 80); ">
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What are your box dimensions doing? To get that kind of sudden change in density, your box dimensions would have to expand astronomically?</blockquote><div><br></div></div><div> Yep.</div><div class="im" style="color: rgb(80, 0, 80); ">
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<br><br>It's also curious that your 425K-atom system only has a PE on the order of 10^5; my systems with 100K-200K have around 10^6 - 10^7; are you sure the minimization is reasonable, and you are not simply seeing the effects of the classic "blowing up" problem?</blockquote>
<div><br></div></div><div>If that was the case would not the NVT also not behave stably? I also agree that 10^5 seems to high. Most of that should come from water though, correct? Why would the water not relax. Maybe I should just expand the box a bit and see what happens?</div>
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What does your trajectory show? If you have multiple proteins or other large species present, does minimization of each component individually prior to system assembly help?</blockquote><div><br></div></div><div>I have one very large protein (antibody). I did do a gas phase minimization of the protein prior to solvation and it does not help.</div>
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