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On 19/09/2011 9:42 AM, Sweta Iyer wrote:
<blockquote
cite="mid:664B02B5-EAB6-4820-8C6B-50150167ED91@wehi.edu.au"
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: normal normal normal 10px/normal
Helvetica; "><font class="Apple-style-span" size="3"><span
class="Apple-style-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>
Sounds like the advice here might be useful. <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>
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