<html><body><div style="color:#000; background-color:#fff; font-family:bookman old style, new york, times, serif;font-size:14pt"><div><span>Dear Mark,</span></div><div><br><span></span></div><div><span>Thank you very much from your reply.</span></div><div><br><span></span></div><div><span>Best Regards</span></div><div><span>Sara</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> Mark Abraham &lt;Mark.Abraham@anu.edu.au&gt;<br> <b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users &lt;gmx-users@gromacs.org&gt; <br> <b><span style="font-weight: bold;">Sent:</span></b> Thursday, February 23, 2012 5:24 AM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re:
 [gmx-users] interface<br> </font> </div> <br>
<div id="yiv449579872">
  

    
  
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    On 22/02/2012 10:34 PM, mohammad agha wrote:
    <blockquote type="cite">
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        255);font-family:bookman old style, new york, times, serif;font-size:14pt;">
        <div><span>Dear Mark,</span></div>
        <div><br>
          <span></span></div>
        <div><span>Thank you very much from your reply.</span></div>
        <div><span>I see a box that the half of it consists of water and
            another half of box is void, but when I run md.mdp for
            production simulation all of water molecules dispersed in
            total of box and I don't see interface and total of box
            filled by water.</span></div>
      </div>
    </blockquote>
    <br>
    What did you expect a liquid in contact with a vacuum to do?<br>
    <br>
    <blockquote type="cite">
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        255);font-family:bookman old style, new york, times, serif;font-size:14pt;">
        <div><br>
          <span></span></div>
        <div><span>Can you help me to construct the air/water interface,
            Please?</span></div>
      </div>
    </blockquote>
    <br>
    First you need to decide how you're going to produce a valid model
    of *air* which is different from a *vacuum*. Then you need to find
    parameters for such a model. Then it's the same kind of approach as
    a mixed-solvent system (see gromacs webpage), only here it will be
    mixed fluid.<br>
    <br>
    Mark<br>
    <br>
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        <div><span><br>
          </span></div>
        <div><span>Best Regards</span></div>
        <div><span>Sara</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>
                Mark Abraham <a rel="nofollow" class="yiv449579872moz-txt-link-rfc2396E" ymailto="mailto:Mark.Abraham@anu.edu.au" target="_blank" href="mailto:Mark.Abraham@anu.edu.au">&lt;Mark.Abraham@anu.edu.au&gt;</a><br>
                <b><span style="font-weight:bold;">To:</span></b>
                Discussion list for GROMACS users
                <a rel="nofollow" class="yiv449579872moz-txt-link-rfc2396E" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">&lt;gmx-users@gromacs.org&gt;</a> <br>
                <b><span style="font-weight:bold;">Sent:</span></b>
                Wednesday, February 22, 2012 12:59 AM<br>
                <b><span style="font-weight:bold;">Subject:</span></b>
                Re: [gmx-users] interface<br>
              </font> </div>
            <br>
            <div id="yiv449579872">
              <div> On 22/02/2012 3:11 AM, mohammad agha wrote:
                <blockquote type="cite">
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                    255);font-family:bookman old style, new york, times, serif;font-size:14pt;">
                    <div>Dear Gromacs Specialists,</div>
                    <div><br>
                    </div>
                    <div>I made a box consists of water with box
                      lengths:&nbsp; 6nm&nbsp; * 6nm&nbsp; * 6nm , then I equilibrated
                      it with NPT ensemble, box size increased to
                      6.66176, then I <font face="Arial"><font size="3">kept
                          the <i>x-</i> and <i>y-</i>dimensions fixed,
                          and double the system size in <i>z as
                            following:</i></font></font></div>
                    <div><font face="Arial"><font size="3"><i>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:</i></font></font></div>
                    <div><font face="Arial"><font size="3"><i>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</i></font></font></div>
                    <div><font face="Arial"><font size="3"><i>and I
                            added one ion to my system, then ran md.mdp
                            for production simulation. <br>
                          </i></font></font></div>
                    <div><font face="Arial"><font size="3"><i>Do I have
                            one air/water interface in my system?</i></font></font></div>
                  </div>
                </blockquote>
                <br>
                You need to use visualization software and see if the
                configuration looks like you intend it to look. You
                certainly don't have an air-water interface if one of
                them is vacuum.<br>
                <br>
                Mark<br>
              </div>
            </div>
            <br>
            -- <br>
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    <br>
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