So, I also check the literature, for water, using flexible SPC model, in Buckingham potential form........<br>How do I use the Buckingham potential form for flexible SPC model? rewriting the itp for water?<br><br>Best<br>XJ<br>
<br><div class="gmail_quote">在 2011年11月15日 下午12:12,xiaojing gong <span dir="ltr">&lt;<a href="mailto:xnzgxj@gmail.com">xnzgxj@gmail.com</a>&gt;</span>写道:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Many thanks<div><div></div><div class="h5"><br><br><div class="gmail_quote">2011/11/15 Mark Abraham <span dir="ltr">&lt;<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>&gt;</span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">


  
    
  
  <div bgcolor="#FFFFFF" text="#000000"><div>
    On 15/11/2011 9:17 PM, xiaojing gong wrote:
    <blockquote type="cite">.......I am not sure.......Do you have some
      suggestions?<br>
    </blockquote>
    <br></div>
    No. The two functional forms are incompatible. GROMACS only allows
    you to define one set of nonbonded parameters, so you can only use
    one functional form in a given simulation. This is fixed in the
    [defaults] section. I suggest you go and look at how the literature
    models CNT plus water.<br><font color="#888888">
    <br>
    Mark</font><div><div></div><div><br>
    <br>
    <blockquote type="cite"><br>
      <div class="gmail_quote">在 2011年11月15日 上午11:05,Mark Abraham <span dir="ltr">&lt;<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>&gt;</span>写
        道:<br>
        <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
          <div bgcolor="#FFFFFF" text="#000000">
            <div> On 15/11/2011 9:03 PM, xiaojing gong wrote:
              <blockquote type="cite">Many thanks for reply.<br>
                Another question, If I use Buckingham potential for CNT,
                and I want to simulate CNT and water, shall I also
                transfer the SPC.itp from LJ to Buckingham potential?<br>
                <br>
                The most important is how to transfer?<br>
                I will appreciate it if you can give me any suggestions.<br>
              </blockquote>
              <br>
            </div>
            How would you compute VDW interactions between carbon atoms
            and water atoms?<br>
            <font color="#888888"> <br>
              Mark</font>
            <div><br>
              <br>
              <blockquote type="cite"><br>
                Best<br>
                XJ<br>
                <br>
                <div class="gmail_quote">2011/11/14 Mark Abraham <span dir="ltr">&lt;<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>&gt;</span><br>
                  <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
                    <div>
                      <div>On 15/11/2011 2:00 AM, xiaojing gong wrote:<br>
                        <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> Hi dear all,<br>
                          For Buckingham potential, there is three
                          parameters A B C<br>
                          In GMX, the units of A B C is the kJ/mol, nm,
                          kJ/mol*nm^6, am I right?<br>
                        </blockquote>
                        <br>
                      </div>
                    </div>
                    Manual section 2.2 defines the units, and 4.1.2
                    defines the functional form.<br>
                    <br>
                    Mark<br>
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