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<DIV dir=ltr>Dear gmxusers,</DIV></DIV>
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<P class=MsoNormal>I have obtained a box of POPC with a starting dimension of 12.48, 12.36, and 6.92 (nm) using genconf –nbox 2 2 1. The original lipid was downloaded from Prof. Tieleman’s site (popc128a.pdb).</P>
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<P class=MsoNormal>My intention is to equilibrate the new bilayer such that the lipids, particularly at the borders where replication occurred, are sufficiently homogenous before I embed a protein into the bilayer. </P>
<P class=MsoNormal> </P>
<P class=MsoNormal> What I did was :-</P>
<P style="TEXT-INDENT: -0.25in" class=MsoListParagraph><SPAN>1)<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN>Energy minimize the new bilayer with the steepest descent method – converged at 131<SUP>st</SUP> step (final potential energy= -8.8059400 e+05)</P>
<P style="TEXT-INDENT: -0.25in" class=MsoListParagraph><SPAN>2)<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN>Perform a brief 100ps NVT on the bilayer with position restraint on the phosphate atom (fc= 1000 on the z axis only). The water layer was found to be non-homogenous after this step.</P>
<P style="TEXT-INDENT: -0.25in" class=MsoListParagraph><SPAN>3)<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN>Perform NPT (still with position restraint on P atom). The water layer became more and more homogenous as I extended the NPT equilibration step. However, I now have a new problem. After 6ns of NPT, I viewed my lipids with VMD and noticed that a few lipid molecules appeared outside the box. I then extended the simulation for another 6 ns and the problem still persists. </P>
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<P class=MsoNormal>I am confused why this phenomena occurred, especially when there was a position restraint on the P atom.</P>
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<P class=MsoNormal>Many thanks for you help.</P>
<P class=MsoNormal> </P>
<P class=MsoNormal>HW </P></DIV></DIV> <<
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