<br><br><div class="gmail_quote">On Wed, Apr 6, 2011 at 11:53 AM, Erik Marklund <span dir="ltr">&lt;<a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">


  
    
    
  
  <div bgcolor="#ffffff" text="#000000">
    Hi,<br>
    <br>
    No we don&#39;t. You can&#39;t have fractions of elementary particles in
    your molecules.<br>
    <br></div></blockquote><div>Dear Erik<br><br>Yes,You are right.It is obvious .<br>But I wanted to simulate a part of my system.for example a part of my protein!<br>I was wrong,we can&#39;t do that <br> <br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div bgcolor="#ffffff" text="#000000">
    Erik<br>
    <br>
    mohsen ramezanpour skrev 2011-04-06 09.13:
    <div><div></div><div class="h5"><blockquote type="cite">Daer Dr.Mark<br>
      <br>
      You are right,But all of them(as I know) have integer charges!<br>
      the problem is simullating a system with partial charges.<br>
      We absolutely have such systems.<br>
      <br>
      <div class="gmail_quote">On Wed, Apr 6, 2011 at 11:22 AM, Mark
        Abraham <span dir="ltr">&lt;<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>&gt;</span>
        wrote:<br>
        <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
          <div text="#000000" bgcolor="#ffffff">
            <div> On 6/04/2011 4:45 PM, mohsen ramezanpour
              wrote:
              <blockquote type="cite">Dear Dr.Justin<br>
                <br>
                What can we do (how can neutralize system) if the total
                charge of our system was not integer?<br>
                I think  there is not any solution and we have to
                simulate a charged system not a neutral.<br>
                Am I right?<br>
              </blockquote>
              <br>
            </div>
            I suspect every tutorial for simulating proteins in water
            deals with the need for counter-ions, and the technique for
            generating them.<br>
            <font color="#888888"> <br>
              Mark</font>
            <div>
              <div><br>
                <br>
                <blockquote type="cite"> Thanks in advance<br>
                  <br>
                  <div class="gmail_quote">On Wed, Apr 6, 2011 at 11:12
                    AM, mohsen ramezanpour <span dir="ltr">&lt;<a href="mailto:ramezanpour.mohsen@gmail.com" target="_blank">ramezanpour.mohsen@gmail.com</a>&gt;</span>
                    wrote:<br>
                    <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Dear Dr.Justin<br>
                      <br>
                      I had the same problem.<br>
                      I modified the charges and charge groupsin the 
                      topology of a drug.the net charge of it is zero(I
                      am sure)<br>
                      though,when I used pdb2gmx it resulted a NOTE like
                      the following:<br>
                      <br>
                      NOTE:The system has non-zero total charge:
                      3.000003e00<br>
                      I continued simulation and ignored it!<br>
                      Because:<br>
                      1- I checked my protein.top and qtot was 3<br>
                      2-the net charge of my drug was 0<br>
                      3-Besides,all charges have 3 digit precision,How
                      can it have 0.000003 additional charge?!<br>
                      <br>
                      What is your point of view?<br>
                      Thanks in advance for your reply
                      <div>
                        <div><br>
                          <br>
                          <br>
                          <div class="gmail_quote">On Wed, Apr 6, 2011
                            at 3:40 AM, Justin A. Lemkul <span dir="ltr">&lt;<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;</span>
                            wrote:<br>
                            <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
                              <div><br>
                                <br>
                                김현식 wrote:<br>
                                <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> <br>
                                  <br>
                                   &gt; Date: Tue, 5 Apr 2011 23:43:19
                                  +1000<br>
                                   &gt; From: <a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
                                   &gt; To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
                                   &gt; Subject: Re: [gmx-users] How to
                                  remove charge of 5e-2 ??<br>
                                   &gt;<br>
                                   &gt; On 5/04/2011 11:17 PM, Hyunsik
                                  wrote:<br>
                                   &gt; &gt; Dear experts,<br>
                                   &gt; &gt;<br>
                                   &gt; &gt; Hi,<br>
                                   &gt; &gt;<br>
                                   &gt; &gt; When prepare a system, the
                                  system had +5.5. So I add 5 CL- ion to
                                  neutralize.<br>
                                   &gt; &gt;<br>
                                   &gt; &gt; But as you know, the Cl
                                  charge is -1 and there still is 5e-2.
                                  how can i remove that.<br>
                                   &gt;<br>
                                   &gt; Your statements are
                                  inconsistent. If you had 5.5 charge
                                  and added five<br>
                                   &gt; chloride ions, you could not end
                                  up with 0.05.<br>
                                  <br>
                                   oh.. I have mistaken.. I had 5.005 of
                                  the system charge.<br>
                                    So even if added five choride ions,
                                  the system charge is not zero. there
                                  was 0.005<br>
                                  <br>
                                   that is partial charge??  If like
                                  that, topology is broken or something
                                  wrong? abnormal??<br>
                                   <br>
                                </blockquote>
                                <br>
                              </div>
                              Maybe, maybe not.  Rounding errors could
                              account for this difference, especially if
                              your system is very large.  Still, you
                              should inspect your topology/topologies
                              for inconsistencies.  If pdb2gmx created
                              the topology, keep an eye on the &quot;qtot&quot;
                              column for a running total of the charge.
                               If you&#39;ve made or adjusted any topologies
                              on your own, double-check your work.  If
                              everything looks correct, then the
                              difference is likely a consequence of
                              floating-point math and nothing more.<br>
                              <br>
                              -Justin
                              <div><br>
                                <br>
                                <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">  Thank you,<br>
                                  <br>
                                   Hyun<br>
                                  <br>
                                   &gt;<br>
                                   &gt; Mark<br>
                                   &gt; --<br>
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                                </blockquote>
                                <br>
                              </div>
                              -- <br>
                              ========================================<br>
                              <br>
                              Justin A. Lemkul<br>
                              Ph.D. Candidate<br>
                              ICTAS Doctoral Scholar<br>
                              MILES-IGERT Trainee<br>
                              Department of Biochemistry<br>
                              Virginia Tech<br>
                              Blacksburg, VA<br>
                              jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a>
                              | (540) 231-9080<br>
                              <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
                              <br>
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                            </blockquote>
                          </div>
                          <br>
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                    </blockquote>
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                  <br>
                </blockquote>
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      </div>
      <br>
    </blockquote>
    <br>
    <br>
    </div></div><pre cols="72">-- 
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
<a href="mailto:erikm@xray.bmc.uu.se" target="_blank">erikm@xray.bmc.uu.se</a>    <a href="http://folding.bmc.uu.se/" target="_blank">http://folding.bmc.uu.se/</a>
</pre>
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