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    On 7/07/2011 6:25 PM, Javier Cerezo wrote:
    <blockquote cite="mid:4E156D6C.9050406@um.es" type="cite">
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      Hi<br>
      <br>
      The large peak in sodium rdf should be a consequence of the
      attractive interaction between Na+ and Cl- and so it seems a
      reasonable plot. Please, try to be a bit more clear and specific
      about your actual problem. You can also post your command line
      arguments for rdf.<br>
      <br>
      Also, in your mdp parameters you've set<br>
      <span id="yiv230548856result_box" class="yiv230548856" lang="en"><span
          title="Click for alternate translations"
          class="yiv230548856hps">freezegrps&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; = Cl fix<br>
          <br>
          This means you have 2 different groups ("Cl" and "fix"), is
          this one your working mdp file?<br>
        </span></span></blockquote>
    <br>
    Indeed. Also, knowing what is in your index groups and the commands
    that produced the graphs is integral to attempting to interpret the
    results, and we're still in the dark.<br>
    <br>
    When you go to a doctor and say "I've got these two lumps, and
    they're different and I'm not sure I should have either of them, or
    that they should look this way", then you're paying the doctor lots
    of money to ask questions about where the lumps are and how long
    they've been there and whether you got bitten by insects and to
    actually look at the lumps and to pat you on the head and say
    they'll probably be gone by the weekend and to maybe invest in some
    mosquito screens and not scratch open one of them. :-)<br>
    <br>
    But when you're hoping someone will give up their time for free to
    help solve your problem... do give as much information as you think
    could possibly be relevant on your first attempt :-)<br>
    <br>
    Mark<br>
    <br>
    <blockquote cite="mid:4E156D6C.9050406@um.es" type="cite"><span
        id="yiv230548856result_box" class="yiv230548856" lang="en"><span
          title="Click for alternate translations"
          class="yiv230548856hps"> <br>
          Javier<br>
          <br>
          <br>
        </span></span><br>
      El 07/07/11 09:49, Saeid Akbarshahi escribi&oacute;:
      <blockquote
        cite="mid:1310024954.71011.YahooMailNeo@web65307.mail.ac2.yahoo.com"
        type="cite">
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                  <div><span></span>Dear All<br>
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                    york,times,serif; font-size: 14pt;">
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                          york,times,serif; font-size: 14pt;">
                          <div> <span id="yiv230548856result_box"
                              class="yiv230548856" lang="en"><span
                                title="Click for alternate translations"
                                class="yiv230548856hps">I</span> <span
                                title="Click for alternate translations"
                                class="yiv230548856hps">want</span> <span
                                title="Click for alternate translations"
                                class="yiv230548856hps">to</span> <span
                                title="Click for alternate translations"
                                class="yiv230548856hps">simulate</span>
                              <span title="Click for alternate
                                translations" class="yiv230548856hps">a</span>&nbsp;</span><span
                              id="yiv230548856result_box"
                              class="yiv230548856" lang="en"><span
                                title="Click for alternate translations"
                                class="yiv230548856hps"></span> <span
                                title="Click for alternate translations"
                                class="yiv230548856hps">box</span></span><span
                              id="yiv230548856result_box"
                              class="yiv230548856" lang="en"> </span><span
                              id="yiv230548856result_box"
                              class="yiv230548856" lang="en"><span
                                title="Click for alternate translations"
                                class="yiv230548856hps">filled</span></span><span
                              id="yiv230548856result_box"
                              class="yiv230548856" lang="en"> <span
                                title="Click for alternate translations"
                                class="yiv230548856hps">water</span><span
                                title="Click for alternate translations"
                                class="yiv230548856hps"></span> <span
                                title="Click for alternate translations"
                                class="yiv230548856hps">that</span> <span
                                title="Click for alternate translations"
                                class="yiv230548856hps">includes 10 </span></span><span
                              id="yiv230548856result_box"
                              class="yiv230548856" lang="en"><span
                                title="Click for alternate translations"
                                class="yiv230548856hps">sodium ion</span></span><span
                              id="yiv230548856result_box"
                              class="yiv230548856" lang="en"><span
                                title="Click for alternate translations"
                                class="yiv230548856hps"></span> <span
                                title="Click for alternate translations"
                                class="yiv230548856hps">and 9</span> <span
                                title="Click for alternate translations"
                                class="yiv230548856hps">chloride</span>
                              <span title="Click for alternate
                                translations" class="yiv230548856hps">ion</span>
                              <span title="Click for alternate
                                translations" class="yiv230548856hps"></span>.<br>
                              <span title="Click for alternate
                                translations" class="yiv230548856hps"></span></span><span
                              id="yiv230548856result_box"
                              class="yiv230548856" lang="en"><span
                                title="Click for alternate translations"
                                class="yiv230548856hps"></span><span
                                title="Click for alternate translations"
                                class="yiv230548856hps"></span><span
                                title="Click for alternate translations"
                                class="yiv230548856hps"></span><span
                                title="Click for alternate translations"
                                class="yiv230548856hps">a chlorine </span></span><span
                              id="yiv230548856result_box"
                              class="yiv230548856" lang="en"><span
                                title="Click for alternate translations"
                                class="yiv230548856hps">fixed</span> <span
                                title="Click for alternate translations"
                                class="yiv230548856hps">place</span></span><span
                              id="yiv230548856result_box"
                              class="yiv230548856" lang="en"> <span
                                title="Click for alternate translations"
                                class="yiv230548856hps">in center of </span><span
                                title="Click for alternate translations"
                                class="yiv230548856hps">box</span></span>
                            simulation<span id="yiv230548856result_box"
                              class="yiv230548856" lang="en"><span
                                title="Click for alternate translations"
                                class="yiv230548856hps"></span><span
                                title="Click for alternate translations"
                                class="yiv230548856hps"></span><span
                                title="Click for alternate translations"
                                class="yiv230548856hps"></span><span
                                title="Click for alternate translations"
                                class="yiv230548856hps"></span><span
                                title="Click for alternate translations"
                                class="yiv230548856hps"></span><span
                                title="Click for alternate translations"
                                class="yiv230548856hps"></span><span
                                title="Click for alternate translations"
                                class="yiv230548856hps"></span><span
                                title="Click for alternate translations"
                                class="yiv230548856hps"></span> <span
                                title="Click for alternate translations"
                                class="yiv230548856hps">to</span> <span
                                title="Click for alternate translations"
                                class="yiv230548856hps">see</span> <span
                                title="Click for alternate translations"
                                class="yiv230548856hps">how it</span> <span
                                title="Click for alternate translations"
                                class="yiv230548856hps">affects</span> <span
                                title="Click for alternate translations"
                                class="yiv230548856hps">the</span> <span
                                title="Click for alternate translations"
                                class="yiv230548856hps">distribution</span>
                              ions .<br>
                              <span title="Click for alternate
                                translations" class="yiv230548856hps">Two</span>
                              <span title="Click for alternate
                                translations" class="yiv230548856hps">graphs</span>
                              <span title="Click for alternate
                                translations" class="yiv230548856hps">were

                                obtained</span> <span title="Click for
                                alternate translations"
                                class="yiv230548856hps">for the</span> <span
                                title="Click for alternate translations"
                                class="yiv230548856hps">distribution</span>
                              <span title="Click for alternate
                                translations" class="yiv230548856hps">of
                                ions</span> than to Cl fix (</span><span
                              id="yiv230548856result_box"
                              class="yiv230548856" lang="en"><span
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                                class="yiv230548856hps">chlorine </span></span><span
                              id="yiv230548856result_box"
                              class="yiv230548856" lang="en"><span
                                title="Click for alternate translations"
                                class="yiv230548856hps">fix</span></span><span
                              id="yiv230548856result_box"
                              class="yiv230548856" lang="en"> </span><span
                              id="yiv230548856result_box"
                              class="yiv230548856" lang="en"> <span
                                title="Click for alternate translations"
                                class="yiv230548856hps">in center of </span><span
                                title="Click for alternate translations"
                                class="yiv230548856hps">box</span></span><span
                              id="yiv230548856result_box"
                              class="yiv230548856" lang="en">)<br>
                              <span title="Click for alternate
                                translations" class="yiv230548856hps">Question</span>
                              :<span title="Click for alternate
                                translations" class="yiv230548856hps"> </span></span><span
                              id="yiv230548856result_box"
                              class="yiv230548856" lang="en"><span
                                title="Click for alternate translations"
                                class="yiv230548856hps">Do</span> <span
                                title="Click for alternate translations"
                                class="yiv230548856hps">not </span></span><span
                              id="yiv230548856result_box"
                              class="yiv230548856" lang="en"><span
                                title="Click for alternate translations"
                                class="yiv230548856hps">very high</span></span><span
                              id="yiv230548856result_box"
                              class="yiv230548856" lang="en"><span
                                title="Click for alternate translations"
                                class="yiv230548856hps"> </span></span><span
                              id="yiv230548856result_box"
                              class="yiv230548856" lang="en"><span
                                title="Click for alternate translations"
                                class="yiv230548856hps">Peak</span> <span
                                title="Click for alternate translations"
                                class="yiv230548856hps">chart</span> <span
                                title="Click for alternate translations"
                                class="yiv230548856hps"></span><span
                                title="Click for alternate translations"
                                class="yiv230548856hps"></span> <span
                                title="Click for alternate translations"
                                class="yiv230548856hps">in rdf sodium</span><span
                                class="yiv230548856" title="Click for
                                alternate translations"> than to Cl fix?</span></span><span></span></div>
                          <div><span id="yiv230548856result_box"
                              class="yiv230548856" lang="en"><span
                                title="Click for alternate translations"
                                class="yiv230548856hps"><br>
                              </span></span></div>
                          <div><span id="yiv230548856result_box"
                              class="yiv230548856" lang="en"><span
                                title="Click for alternate translations"
                                class="yiv230548856hps">The total</span>
                              <span title="Click for alternate
                                translations" class="yiv230548856hps">electrical
                                charge = 10 + (-10) = 0<br>
                              </span></span></div>
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                              york,times,serif; font-size: 14pt;">
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                                    class="yiv230548856hps">Box : 2.65 *</span></span><span
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                                    class="yiv230548856hps">2.65 *</span></span><span
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                                    class="yiv230548856hps">2.65 nm<br>
                                    force field : AMBER99SB-ILDN<br>
                                  </span></span></div>
                              <div><span id="yiv230548856result_box"
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                                    class="yiv230548856hps">Number of Na
                                    : 10 <br>
                                  </span></span></div>
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                                    class="yiv230548856hps">Number of </span></span><span
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                                    class="yiv230548856hps">Cl : 9</span></span></div>
                              <div><span id="yiv230548856result_box"
                                  class="yiv230548856" lang="en"><span
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                                    class="yiv230548856hps">Number of </span></span><span
                                  id="yiv230548856result_box"
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                                    class="yiv230548856hps">Cl fix&nbsp; : 1</span></span></div>
                              <div><span id="yiv230548856result_box"
                                  class="yiv230548856" lang="en"><span
                                    title="Click for alternate
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                                    class="yiv230548856hps">Time
                                    simulation : 4 ns</span></span></div>
                              <div><span id="yiv230548856result_box"
                                  class="yiv230548856" lang="en"><span
                                    title="Click for alternate
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                                    class="yiv230548856hps">Water :
                                    TIP3P<br>
                                    file.mdp<br>
                                    ; Run parameters<br>
                                    integrator&nbsp;&nbsp;&nbsp; = md-vv&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; <br>
                                    nsteps&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; = 2000000&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; <br>
                                    dt&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; = 0.002&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; ; 2 fs<br>
                                    constraints&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp; none&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; <br>
                                    ns_type&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; = grid&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; <br>
                                    nstlist&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; = 5&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; <br>
                                    rlist&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; = 1.0&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; <br>
                                    rcoulomb&nbsp;&nbsp;&nbsp; = 1.0&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; <br>
                                    rvdw&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; = 1.0&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; <br>
                                    ; Electrostatics<br>
                                    coulombtype&nbsp;&nbsp;&nbsp; = PME&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; <br>
                                    pme_order&nbsp;&nbsp;&nbsp; = 4&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; <br>
                                    fourierspacing&nbsp;&nbsp;&nbsp; = 0.15&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; <br>
                                    ewald_rtol&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; = 1e-05<br>
                                    optimize_fft&nbsp;&nbsp;&nbsp; = yes<br>
                                    ; Temperature coupling is on<br>
                                    tcoupl&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; = nose-hoover&nbsp;&nbsp;&nbsp; <br>
                                    tc-grps&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; = System&nbsp;&nbsp;&nbsp; <br>
                                    tau_t&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; = 0.5&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; <br>
                                    ref_t&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; = 298 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; <br>
                                    pbc&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; = xyz&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; <br>
                                    DispCorr&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; = EnerPres<br>
                                    vdw-type&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; = Cut-off<br>
                                    freezegrps&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; = Cl fix<br>
                                    freezedim&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; = Y Y Y<br>
                                    <br>
                                  </span></span></div>
                              <div><span id="yiv230548856result_box"
                                  class="yiv230548856" lang="en"><span
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                                    class="yiv230548856hps">Kind Regard<br>
                                  </span></span></div>
                            </div>
                          </div>
                        </div>
                      </div>
                      <br>
                      <br>
                    </div>
                  </div>
                </div>
              </div>
              <br>
              <br>
            </div>
          </div>
        </div>
      </blockquote>
      <br>
      <pre class="moz-signature" cols="72">-- 
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tlf.(+34)868887434</pre>
    </blockquote>
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