Dear Justin,<br><br>When I used the energy mininized system for NPT annealing with position restraints on lipids and there was no separation. So, I think I can proceed now to equiliration phase 2 (1-ns NPT equilibration-NPT) and then run the Molecular Dynamics for data collection(1ns).What do you suggest, is it the right way i am following..as i will be not be using NVT equillibration anywhere through out the process.<br>
<br>Thanks,<br><br>Ram<br><br><br><div class="gmail_quote">On Fri, Sep 25, 2009 at 11:23 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;">
<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><div class="im">
As suggested, i increased the force constant in the Z dimension from 1000 to 10000, and did the NVT equillibration, but still the gap existed, then i gave the output of nvt equillibration that is nvt.gro as input for the NPT anneling simulation (suggested as with position constraints, 1000) and simulated and here also i had gap .between layers when npt.gro was viewed in VMD.<br>
<br>
I have a query that is can I use nvt equllibrated system as input for NPT simualated annealing or should I use the initial ionized and minimized system for the NPT annaelated simulation, as the gap is still persisting...<br>
<br>
</div></blockquote>
<br>
Use the energy-minimized system as the input into annealing. I have no idea why this separation would be happening in this system, unless the box has been prepared improperly. I chose the KALP-DPPC system because it is very robust in everything we've tried to subject it to.<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 Thu, Sep 24, 2009 at 4:16 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>
ram bio wrote:<br>
<br></div><div><div></div><div class="h5">
Dear Justin,<br>
<br>
As suggested in the tutorial by you i applied the lipid position<br>
restraints, while running the NVT equillibration, but after the<br>
job is finished, when i observed the nvt.gro file in VMD, still<br>
there is a gap between the lipid bilayers but this time the gap<br>
is not so large as it was in the earlier run (as discussed<br>
earlier in previous email).<br>
<br>
As I was already running the NPT equillibration(which I obtained<br>
after the earlier NVT job, which ended in large gap between<br>
layers), i just wanted to observe it and here there is no gap in<br>
between the layers i.e. in npt.gro.<br>
<br>
Please suggest me what to do to lower the gap after NVT<br>
equillibration even after applying the lipid restraints and is<br>
it ok for my NPT equillibration as there are no gaps between the<br>
layers after this NPT equillibration.<br>
<br>
<br>
The gap arises because the lipids (when free to move) are attracted<br>
to the water above and below the bilayer. If the protein is<br>
restrained, it doesn't move. The box size in NVT is fixed, so the<br>
system is trying to fill it. It could be that your box was<br>
inappropriately assigned (too large), but maybe not.<br>
<br>
I am surprised that, even when using position restraints, the lipids<br>
still separated at all. Did you use the lipid_posre.itp file that I<br>
provide on the tutorial site? It has always worked well for me in<br>
such cases. You could also try increasing the force constant in the<br>
z-dimension.<br>
<br>
The other option is to do NPT simulated annealing, as I also suggest<br>
in the troubleshooting page. Using NPT allows the box to deform in<br>
response to the system, so you will probably get less weird<br>
behavior. I have found that both NVT with PR and simulated<br>
annealing can get the job done.<br>
<br>
-Justin<br>
<br>
Thanks<br>
<br>
Ram<br>
<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><br></div></div>
<mailto:<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><div class="im"><br>
<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<br>
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<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><div></div><div class="h5">
<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>
<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<br>
after<br>
the NVT equillibration phase. The mdrun was proper<br>
without<br>
any warnings or errors, but when i visuallized the<br>
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<br>
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.<br>
Please<br>
see the "Advanced Troubleshooting" page (part of the<br>
tutorial!),<br>
because I specifically address the issue of a bilayer<br>
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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-- ========================================<br>
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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> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<br>
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<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>
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