<p>Also it is possible that there might be a problem with setting up the membrane. Have you tried running the membrane without protein?<br>
-Shay</p>
<div class="gmail_quote">On Sep 19, 2011 3:32 AM, "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br type="attribution">> <br>> <br>> Michael Daily wrote:<br>>> Unfortunately genbox will put waters anywhere there is a space, <br>
>> including inside the membrane. This can easily be fixed by making a <br>>> script to remove waters that are z +/- ~2 nm from the membrane center <br>>> (you should run g_density on the system to figure out the optimal <br>
>> distance filter). You can run this after running genbox.<br>>> <br>> <br>> An even simpler approach is outlined here:<br>> <br>> <a href="http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations#Adding_waters_with_genbox">http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations#Adding_waters_with_genbox</a><br>
> <br>> It seems to me that the original problem either derives from incorrect <br>> construction, incorrect application of position restraints, or as Mark <br>> suggested, an artifact of PBC.<br>> <br>> -Justin<br>
> <br>>> On Sun, Sep 18, 2011 at 5:12 PM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a> <br>>> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>>> wrote:<br>
>> <br>>> On 19/09/2011 9:42 AM, Sweta Iyer wrote:<br>>>> Hi,<br>>>> I embedded my protein of interest into a DMPC membrane by the<br>>>> g_membed tool with the following command:<br>
>>> g membed -f input.tpr -p system.top -n index.ndx -xyinit 0.1<br>>>> -xyend 1.0 -nxy 1000 -zinit 1.1 -zend 1.0 -nz 100<br>>>><br>>>> I then energy minimized the resultant structure for 1 ns before<br>
>>> the position restraint dynamics and the productive run.<br>>>> My structure looks fine after the em. However, when I do the PR<br>>>> and look at the structure it looks weird in that half of the<br>
>>> protein is hanging out of the membrane and there seems to be a<br>>>> patch of water molecules that seem to have entered the membrane.<br>>>><br>>>> I have no clue what must be possibly going wrong here. Should I<br>
>>> have equilibrated the system for longer than 1ns or is it<br>>>> something wrong with the membrane insertion.<br>>>><br>>> <br>>> Sounds like the advice here might be useful.<br>
>> <a href="http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions">http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions</a><br>>> <br>>> Mark<br>>> <br>
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>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>>> Please search the archive at<br>>> <a href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
>> Please don't post (un)subscribe requests to the list. Use the<br>>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br>>> <mailto:<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>.<br>
>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a><br>>> <br>>> <br>>> <br>>> <br>>> -- <br>>> ====================================<br>
>> Michael D. Daily<br>>> Postdoctoral research associate<br>>> Pacific Northwest National Lab (PNNL)<br>>> 509-375-4581<br>>> (formerly Qiang Cui group, University of Wisconsin-Madison)<br>>> <br>
> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<br>> Department of Biochemistry<br>
> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]<a href="http://vt.edu">vt.edu</a> | (540) 231-9080<br>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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> Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>
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