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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">What does it look like when you visualise the coordinate file? That is how you can answer that question, as we certainly can’t.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">And as you will soon find out, you cannot have a single interface in a simulation box, you have to have two.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Catch ya,<br>
<br>
Dr. Dallas Warren<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Medicinal Chemistry and Drug Action<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Monash Institute of Pharmaceutical Sciences</span><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
dallas.warren@monash.edu<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">+61 3 9903 9304<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to resemble a nail.</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">
<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org]
<b>On Behalf Of </b>mohammad agha<br>
<b>Sent:</b> Wednesday, 22 February 2012 3:12 AM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> [gmx-users] interface<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:14.0pt;font-family:"Bookman Old Style","serif";color:black">Dear Gromacs Specialists,<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:14.0pt;font-family:"Bookman Old Style","serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:14.0pt;font-family:"Bookman Old Style","serif";color:black">I made a box consists of water with box lengths: 6nm * 6nm * 6nm , then I equilibrated it with NPT ensemble, box size increased
to 6.66176, then I </span><span style="font-family:"Arial","sans-serif";color:black">kept the
<i>x-</i> and <i>y-</i>dimensions fixed, and double the system size in <i>z as following:</i></span><span style="font-size:14.0pt;font-family:"Bookman Old Style","serif";color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><i><span style="font-family:"Arial","sans-serif";color:black">editconf -f pr1.gro -o newbox1.gro -box 6.66176 6.66176 13.32352 -center 3.33088 3.33088 3.33088<br>
Next that, I placed one surfactant in center of water phase as following:</span></i><span style="font-size:14.0pt;font-family:"Bookman Old Style","serif";color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><i><span style="font-family:"Arial","sans-serif";color:black">editconf -f surfactant.gro -o newbox-cta.gro -box 6.66176 6.66176 13.32352 -center 3.33088 3.33088 1.66544<br>
genbox -cp newbox-cta.gro -cs newbox1.gro -o newbox2.gro</span></i><span style="font-size:14.0pt;font-family:"Bookman Old Style","serif";color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><i><span style="font-family:"Arial","sans-serif";color:black">and I added one ion to my system, then ran md.mdp for production simulation.
</span></i><span style="font-size:14.0pt;font-family:"Bookman Old Style","serif";color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><i><span style="font-family:"Arial","sans-serif";color:black">Do I have one air/water interface in my system?</span></i><span style="font-size:14.0pt;font-family:"Bookman Old Style","serif";color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><i><span style="font-family:"Arial","sans-serif";color:black">Please help me.</span></i><span style="font-size:14.0pt;font-family:"Bookman Old Style","serif";color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:14.0pt;font-family:"Bookman Old Style","serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><i><span style="font-family:"Arial","sans-serif";color:black">Best Regards</span></i><span style="font-size:14.0pt;font-family:"Bookman Old Style","serif";color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><i><span style="font-family:"Arial","sans-serif";color:black">Sara</span></i><span style="font-size:14.0pt;font-family:"Bookman Old Style","serif";color:black"><o:p></o:p></span></p>
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