Dear Justin, <br><br>As suggested in the tutorial by you i applied the lipid <font face="Arial"><font size="3">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>Thanks<br><br>Ram<br></font></font><br><div class="gmail_quote">On Tue, Sep 22, 2009 at 8:25 PM, ram bio <span dir="ltr"><<a href="mailto:rmbio861@gmail.com">rmbio861@gmail.com</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;">
Dear Justin,<br><br>Thanks for the suggestion, will try to apply position restraints on lipid as mentioned in the advanced trouble shooting section.<br><font color="#888888"><br>Ram</font><div><div></div><div class="h5"><br>
<br><div class="gmail_quote">On Tue, Sep 22, 2009 at 8:08 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">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><div></div><div><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 Gromacs Users,<br>
<br>
I am following the justin tutorial on KALP-15 in lipid bilayer, I have a query regarding the nvt.gro that is after the NVT equillibration phase. The mdrun was proper without any warnings or errors, but when i visuallized the nvt.gro in VMD, i found that the peptide is intact in between the bilayers, but the the two layers got separated or else it is like the peptide bridging the the two halves of the lipid bilayer with gap in between the layers and also found few water molecules to the sides of the peptide or in the gap mentioned betwwn the layers.<br>
<br>
Please let me know is the simulation going on normally or there is an defect or wrong going on, as the nvt equillibration was proper as i think i continued for the next equillibration that is npt for 1ns.<br>
<br>
</blockquote>
<br></div></div>
You shouldn't continue blindly if you get weird results. Please see the "Advanced Troubleshooting" page (part of the tutorial!), 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>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Ram<br>
<br>
<br>
------------------------------------------------------------------------<br>
<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</blockquote>
<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>
<br>
========================================<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</blockquote></div><br>
</div></div></blockquote></div><br>