<html><body><div style="color:#000; background-color:#fff; font-family:bookman old style, new york, times, serif;font-size:14pt"><div><span>Dear Dr. Warren,</span></div><div><br><span></span></div><div><span>Thank you very much from your response. <br></span></div><div><span>When I see the coordinate file, there is a box consists of water in half of it and another half of box is void, but when I do md.mdp for production simulation, all of water molecules are dispersed in total of box.</span></div><div><span><br></span></div><div><span>Can you help me for construct the air/water interface, Please?</span></div><div><br><span></span></div><div><span>Best Regards</span></div><div><span>Sara<br></span></div><div><br></div> <div style="font-family: bookman old style, new york, times, serif; font-size: 14pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div dir="ltr"> <font size="2" face="Arial"> <hr size="1">
<b><span style="font-weight:bold;">From:</span></b> Dallas Warren <Dallas.Warren@monash.edu><br> <b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Wednesday, February 22, 2012 4:26 AM<br> <b><span style="font-weight: bold;">Subject:</span></b> RE: [gmx-users] interface<br> </font> </div> <br>
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<div class="yiv497951860MsoNormal"><span style="font-size:11.0pt;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.</span></div>
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<div class="yiv497951860MsoNormal"><span style="font-size:11.0pt;color:#1F497D;">And as you will soon find out, you cannot have a single interface in a simulation box, you have to have two.</span></div>
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<div class="yiv497951860MsoNormal"><span style="font-size:10.0pt;color:#1F497D;">Catch ya,<br>
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Dr. Dallas Warren</span></div>
<div class="yiv497951860MsoNormal"><span style="font-size:10.0pt;color:#1F497D;">Medicinal Chemistry and Drug Action</span></div>
<div class="yiv497951860MsoNormal"><span style="font-size:10.0pt;color:#1F497D;">Monash Institute of Pharmaceutical Sciences</span><span style="font-size:10.0pt;color:#1F497D;">, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
dallas.warren@monash.edu</span></div>
<div class="yiv497951860MsoNormal"><span style="font-size:10.0pt;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;color:#1F497D;">
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<div class="yiv497951860MsoNormal"><b><span style="font-size:10.0pt;">From:</span></b><span style="font-size:10.0pt;"> 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</span></div>
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<div class="yiv497951860MsoNormal" style="background:white;"><span style="font-size:14.0pt;color:black;">Dear Gromacs Specialists,</span></div>
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<div class="yiv497951860MsoNormal" style="background:white;"><span style="font-size:14.0pt;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="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;color:black;"></span></div>
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<div class="yiv497951860MsoNormal" style="background:white;"><i><span style="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;color:black;"></span></div>
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<div class="yiv497951860MsoNormal" style="background:white;"><i><span style="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;color:black;"></span></div>
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<div class="yiv497951860MsoNormal" style="background:white;"><i><span style="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;color:black;"></span></div>
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<div class="yiv497951860MsoNormal" style="background:white;"><i><span style="color:black;">Do I have one air/water interface in my system?</span></i><span style="font-size:14.0pt;color:black;"></span></div>
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<div class="yiv497951860MsoNormal" style="background:white;"><i><span style="color:black;">Please help me.</span></i><span style="font-size:14.0pt;color:black;"></span></div>
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<div class="yiv497951860MsoNormal" style="background:white;"><span style="font-size:14.0pt;color:black;"> </span></div>
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<div class="yiv497951860MsoNormal" style="background:white;"><i><span style="color:black;">Best Regards</span></i><span style="font-size:14.0pt;color:black;"></span></div>
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<div class="yiv497951860MsoNormal" style="background:white;"><i><span style="color:black;">Sara</span></i><span style="font-size:14.0pt;color:black;"></span></div>
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