Dear Justin,<br><br>Thanks for the options and suggestions, will be back after some trials with modelled proteins.<br><br>Ram<br><br><div class="gmail_quote">On Mon, Sep 28, 2009 at 6:17 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">
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>
</div></blockquote>
<br>
I think that should be fine. There is really no prescribed way to do equilibration, necessarily. Everyone has their own method. If you can stabilize the temperature and pressure prior to data collection, then you've done enough, in general. Just be aware that my definition of "data collection" simply means that you're remove restraints from anything that was previously restrained. Collecting data for membrane protein systems often occurs after 10-20 ns (or more), to allow for re-orientation of lipids, which is very slow.<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>
<br>
On Fri, Sep 25, 2009 at 11:23 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>
Dear Justin,<br>
<br>
As suggested, i increased the force constant in the Z dimension<br>
from 1000 to 10000, and did the NVT equillibration, but still<br>
the gap existed, then i gave the output of nvt equillibration<br>
that is nvt.gro as input for the NPT anneling simulation<br>
(suggested as with position constraints, 1000) and simulated and<br>
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<br>
input for NPT simualated annealing or should I use the initial<br>
ionized and minimized system for the NPT annaelated simulation,<br>
as the gap is still persisting...<br>
<br>
<br>
Use the energy-minimized system as the input into annealing. I have<br>
no idea why this separation would be happening in this system,<br>
unless the box has been prepared improperly. I chose the KALP-DPPC<br>
system because it is very robust in everything we've tried to<br>
subject it to.<br>
<br>
-Justin<br>
<br>
Thanks<br>
<br>
Ram<br>
<br>
<br>
On Thu, Sep 24, 2009 at 4:16 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>
<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<br>
position<br>
restraints, while running the NVT equillibration, but<br>
after the<br>
job is finished, when i observed the nvt.gro file in VMD,<br>
still<br>
there is a gap between the lipid bilayers but this time<br>
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<br>
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<br>
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<br>
and is<br>
it ok for my NPT equillibration as there are no gaps<br>
between the<br>
layers after this NPT equillibration.<br>
<br>
<br>
The gap arises because the lipids (when free to move) are<br>
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<br>
lipids<br>
still separated at all. Did you use the lipid_posre.itp file<br>
that I<br>
provide on the tutorial site? It has always worked well for<br>
me in<br>
such cases. You could also try increasing the force constant<br>
in the<br>
z-dimension.<br>
<br>
The other option is to do NPT simulated annealing, as I also<br>
suggest<br>
in the troubleshooting page. Using NPT allows the box to<br>
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<br>
<<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>><br>
<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>>><br>
<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>><br>
<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><div></div><div class="h5">
<br>
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<br>
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>
<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>>><br>
<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>><br>
<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<br>
in lipid<br>
bilayer, I have a query regarding the nvt.gro<br>
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<br>
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<br>
of the lipid<br>
bilayer with gap in between the layers and<br>
also found few<br>
water molecules to the sides of the peptide or<br>
in the gap<br>
mentioned betwwn the layers.<br>
<br>
Please let me know is the simulation going on<br>
normally or<br>
there is an defect or wrong going on, as the nvt<br>
equillibration was proper as i think i<br>
continued for the<br>
next equillibration that is npt for 1ns.<br>
<br>
<br>
You shouldn't continue blindly if you get weird<br>
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>
------------------------------------------------------------------------<br>
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ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
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-- ========================================<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> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540)<br>
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<br>
========================================<br>
<br>
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<br></div></div><div class="im">
-- ========================================<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> <<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></div><div><div></div><div class="h5">
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
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