Unfortunately genbox will put waters anywhere there is a space, including inside the membrane. This can easily be fixed by making a script to remove waters that are z +/- ~2 nm from the membrane center (you should run g_density on the system to figure out the optimal distance filter). You can run this after running genbox.<br>
<br><div class="gmail_quote">On Sun, Sep 18, 2011 at 5:12 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div bgcolor="#FFFFFF" text="#000000"><div class="im">
On 19/09/2011 9:42 AM, Sweta Iyer wrote:
<blockquote type="cite">Hi,
<div>I embedded my protein of interest into a DMPC membrane by the
g_membed tool with the following command:</div>
<div>
<div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"><font size="3"><span style="font-size:12px">g membed
-f input.tpr -p system.top -n index.ndx -xyinit 0.1
-xyend 1.0 -nxy 1000 -zinit 1.1 -zend 1.0 -nz 100</span></font></div>
</div>
<div><br>
</div>
<div>I then energy minimized the resultant structure for 1 ns
before the position restraint dynamics and the productive run.</div>
<div>My structure looks fine after the em. However, when I do the
PR and look at the structure it looks weird in that half of the
protein is hanging out of the membrane and there seems to be a
patch of water molecules that seem to have entered the membrane.</div>
<div><br>
</div>
<div>I have no clue what must be possibly going wrong here. Should
I have equilibrated the system for longer than 1ns or is it
something wrong with the membrane insertion.</div>
<br>
</blockquote>
<br></div>
Sounds like the advice here might be useful. <a href="http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions" target="_blank">http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions</a><br>
<font color="#888888">
<br>
Mark<br>
</font></div>
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(formerly Qiang Cui group, University of Wisconsin-Madison)</font></font><br>