Dear Justin,<br><br>Thanks, will try the options described.<br><br>Ram<br><br><div class="gmail_quote">On Thu, Sep 24, 2009 at 4:16 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>
ram bio wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Justin,<br>
<br>
As suggested in the tutorial by you i applied the lipid position restraints, while running the NVT equillibration, but after the job is finished, when i observed the nvt.gro file in VMD, still there is a gap between the lipid bilayers but this time the gap is not so large as it was in the earlier run (as discussed earlier in previous email).<br>
<br>
As I was already running the NPT equillibration(which I obtained after the earlier NVT job, which ended in large gap between layers), i just wanted to observe it and here there is no gap in between the layers i.e. in npt.gro.<br>
<br>
Please suggest me what to do to lower the gap after NVT equillibration even after applying the lipid restraints and is it ok for my NPT equillibration as there are no gaps between the layers after this NPT equillibration.<br>
<br>
</blockquote>
<br></div>
The gap arises because the lipids (when free to move) are attracted to the water above and below the bilayer. If the protein is restrained, it doesn't move. The box size in NVT is fixed, so the system is trying to fill it. It could be that your box was inappropriately assigned (too large), but maybe not.<br>
<br>
I am surprised that, even when using position restraints, the lipids still separated at all. Did you use the lipid_posre.itp file that I provide on the tutorial site? It has always worked well for me in such cases. You could also try increasing the force constant in the z-dimension.<br>
<br>
The other option is to do NPT simulated annealing, as I also suggest in the troubleshooting page. Using NPT allows the box to deform in response to the system, so you will probably get less weird behavior. I have found that both NVT with PR and simulated annealing can get the job done.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thanks<br>
<br>
Ram<div class="im"><br>
<br>
On Tue, Sep 22, 2009 at 8:25 PM, ram bio <<a href="mailto:rmbio861@gmail.com" target="_blank">rmbio861@gmail.com</a> <mailto:<a href="mailto:rmbio861@gmail.com" target="_blank">rmbio861@gmail.com</a>>> wrote:<br>
<br>
Dear Justin,<br>
<br>
Thanks for the suggestion, will try to apply position restraints on<br>
lipid as mentioned in the advanced trouble shooting section.<br>
<br>
Ram<br>
<br>
<br>
On Tue, Sep 22, 2009 at 8:08 PM, Justin A. Lemkul <<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>>> wrote:<br>
<br>
<br>
<br>
ram bio wrote:<br>
<br>
Dear Gromacs Users,<br>
<br>
I am following the justin tutorial on KALP-15 in lipid<br>
bilayer, I have a query regarding the nvt.gro that is after<br>
the NVT equillibration phase. The mdrun was proper without<br>
any warnings or errors, but when i visuallized the nvt.gro<br>
in VMD, i found that the peptide is intact in between the<br>
bilayers, but the the two layers got separated or else it is<br>
like the peptide bridging the the two halves of the lipid<br>
bilayer with gap in between the layers and also found few<br>
water molecules to the sides of the peptide or in the gap<br>
mentioned betwwn the layers.<br>
<br>
Please let me know is the simulation going on normally or<br>
there is an defect or wrong going on, as the nvt<br>
equillibration was proper as i think i continued for the<br>
next equillibration that is npt for 1ns.<br>
<br>
<br>
You shouldn't continue blindly if you get weird results. Please<br>
see the "Advanced Troubleshooting" page (part of the tutorial!),<br>
because I specifically address the issue of a bilayer separating:<br>
<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/advanced_troubleshooting.html" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/advanced_troubleshooting.html</a><br>
<br>
-Justin<br>
<br>
Ram<br>
<br>
<br>
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Justin A. Lemkul<br>
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Virginia Tech<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>
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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