<div dir="ltr">Dear Ben,<div><br></div><div>Here is the link for the 28 ps trajectory with only 28 steps (representing the geometry after each ps). Kindly, have a look. I am not able to send the xyz file directly to the list as it is > 256 KB (it is 442 KB).</div><div><br></div><div>Thanking you,</div><div>Sharma.</div><div><br></div><div><a href="https://drive.google.com/open?id=0B7l7TJgy0hzhWmxEY1lodEdUdUE">https://drive.google.com/open?id=0B7l7TJgy0hzhWmxEY1lodEdUdUE</a><br></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><font color="#000000"><br></font></div><div dir="ltr"><font color="#000000"><br></font></div><div dir="ltr"><font color="#000000"><br></font></div><div dir="ltr"><font color="#000000"><br></font></div><div dir="ltr"><font color="#000000">--------------------------------------------------------------------<br><font size="2" face="arial, helvetica, sans-serif">Sharma</font></font></div><div dir="ltr"><font color="#000000" face="arial, helvetica, sans-serif"><a href="http://www.chem.rochester.edu/groups/huo/people/" target="_blank">http://www.chem.rochester.edu/groups/huo/people/</a></font></div><div dir="ltr"><br></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Thu, Aug 4, 2016 at 1:21 PM, Sharma SRK Chaitanya Yamijala <span dir="ltr"><<a href="mailto:sharmajncasr@gmail.com" target="_blank">sharmajncasr@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><br clear="all"><div><div data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><font color="#000000"><br></font></div><div dir="ltr"><font color="#000000"><br></font></div><div dir="ltr"><font color="#000000"><br></font></div><div dir="ltr"><font color="#000000"><br></font></div><div dir="ltr"><font color="#000000">------------------------------<wbr>------------------------------<wbr>--------<br><font size="2" face="arial, helvetica, sans-serif">Sharma</font></font></div><div dir="ltr"><font color="#000000" face="arial, helvetica, sans-serif"><a href="http://www.chem.rochester.edu/groups/huo/people/" target="_blank">http://www.chem.rochester.edu/<wbr>groups/huo/people/</a></font></div><div dir="ltr"><br></div></div></div></div></div></div></div></div></div><div><div class="h5">
<br><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">Sharma SRK Chaitanya Yamijala</b> <span dir="ltr"><<a href="mailto:sharmajncasr@gmail.com" target="_blank">sharmajncasr@gmail.com</a>></span><br>Date: Thu, Aug 4, 2016 at 1:18 PM<br>Subject: Re: [DFTB-Plus-User] Molecules being separated during MD<br>To: User list for DFTB+ related questions <<a href="mailto:dftb-plus-user@mailman.zfn.uni-bremen.de" target="_blank">dftb-plus-user@mailman.zfn.<wbr>uni-bremen.de</a>><br><br><br><div dir="ltr">Hi Ben,<div><br></div><div>I am confirming that the molecules are moving apart from each other after 10 ps (even when the initial geometry is optimized with DFTB+).</div><div><br></div><div>Thanking you,</div><div>Sincerely,<br>Sharma.</div><div><br></div><div>P.S.: I tried to attach images yesterday, but it didn't work. Now, I am sending the xyz file with each frame corresponding to the MD geometry after each picosecond.</div></div><div class="gmail_extra"><br clear="all"><div><div data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><font color="#000000"><br></font></div><div dir="ltr"><font color="#000000"><br></font></div><div dir="ltr"><font color="#000000"><br></font></div><div dir="ltr"><font color="#000000"><br></font></div><div dir="ltr"><font color="#000000">------------------------------<wbr>------------------------------<wbr>--------<br><font size="2" face="arial, helvetica, sans-serif">Sharma</font></font></div><div dir="ltr"><font color="#000000" face="arial, helvetica, sans-serif"><a href="http://www.chem.rochester.edu/groups/huo/people/" target="_blank">http://www.chem.rochester.edu/<wbr>groups/huo/people/</a></font></div><div dir="ltr"><br></div></div></div></div></div></div></div></div></div><div><div>
<br><div class="gmail_quote">On Wed, Aug 3, 2016 at 3:04 PM, Sharma SRK Chaitanya Yamijala <span dir="ltr"><<a href="mailto:sharmajncasr@gmail.com" target="_blank">sharmajncasr@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Dear Ben,<div><br></div><div>Thanks for the reply. When compared to the earlier trajectory (without dftb optimization), the system is not moving apart that much. However, I could see that relative position of both the molecules is changed as given in the attached images (0 and 3ps).</div><div><br></div><div>At 3 ps, system without dftb optimization also behaved in a similar way, and hence, I expected that the molecules move apart as observed eariler. However, now (after 4ps), I could see that the system is still intact (though polymer has moved from the base of fullerene to the branches of fullerene, which maybe the effect of dynamics and dispersion interactions).</div><div><br></div><div>In order to check these effects, I am continuing my run (till 30 ps). I will update you.</div><div><br></div><div>Kindly, let me know whether your observation till 3ps is similar to what I have observed or not.</div><div><br></div><div>Thanking you,</div><div>Sincerely,</div><div>Sharma.</div></div><div class="gmail_extra"><br clear="all"><div><div data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><font color="#000000"><br></font></div><div dir="ltr"><font color="#000000"><br></font></div><div dir="ltr"><font color="#000000"><br></font></div><div dir="ltr"><font color="#000000"><br></font></div><div dir="ltr"><font color="#000000">------------------------------<wbr>------------------------------<wbr>--------<br><font size="2" face="arial, helvetica, sans-serif">Sharma</font></font></div><div dir="ltr"><font color="#000000" face="arial, helvetica, sans-serif"><a href="http://www.chem.rochester.edu/groups/huo/people/" target="_blank">http://www.chem.rochester.edu/<wbr>groups/huo/people/</a></font></div><div dir="ltr"><br></div></div></div></div></div></div></div></div></div><div><div>
<br><div class="gmail_quote">On Wed, Aug 3, 2016 at 2:07 PM, Ben Hourahine <span dir="ltr"><<a href="mailto:benjamin.hourahine@strath.ac.uk" target="_blank">benjamin.hourahine@strath.ac.<wbr>uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
  
    
  
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    <p>Hello Sharma,</p>
    <p>after the 30k steps the sulfur containing molecule rotates and
      move slightly away for me. The distance from the fullerene
      increases from 0.34 nm to 0.42 nm, is this the scale of movement
      you mean?</p>
    <p>Regards</p>
    <p>Ben<br>
    </p><div><div>
    <div>On 03/08/16 18:49, Sharma SRK Chaitanya
      Yamijala wrote:<br>
    </div>
    <blockquote type="cite">
      
      <div dir="ltr">Dear Ben,
        <div><br>
        </div>
        <div>After running 3 ps trajectory (after optimizing the initial
          geometry with DFTB), I observed similar behavior as mentioned
          in the earlier e-mails (molecules moving apart). Could you
          please confirm whether your calculation also lead to the
          similar result or not?</div>
        <div><br>
        </div>
        <div>Thanking you,<br>
          Sincerely,</div>
        <div>Sharma.</div>
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                        <div dir="ltr"><font color="#000000">------------------------------<wbr>------------------------------<wbr>--------<br>
                            <font face="arial, helvetica, sans-serif" size="2">Sharma</font></font></div>
                        <div dir="ltr"><font color="#000000" face="arial, helvetica, sans-serif"><a href="http://www.chem.rochester.edu/groups/huo/people/" target="_blank">http://www.chem.rochester.edu/<wbr>groups/huo/people/</a></font></div>
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        <div class="gmail_quote">On Mon, Aug 1, 2016 at 6:27 PM, Sharma
          SRK Chaitanya Yamijala <span dir="ltr"><<a href="mailto:sharmajncasr@gmail.com" target="_blank">sharmajncasr@gmail.com</a>></span>
          wrote:<br>
          <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
            <div dir="ltr">Dear Ben,
              <div><br>
              </div>
              <div>Thank you for this point and for your time. I will
                also give a try in the way you mentioned.</div>
              <div><br>
              </div>
              <div>Thanking you,</div>
              <div>Sincerely,</div>
              <div>Sharma.</div>
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                              <div dir="ltr"><font color="#000000">------------------------------<wbr>------------------------------<wbr>--------<br>
                                  <font face="arial, helvetica,
                                    sans-serif" size="2">Sharma</font></font></div>
                              <div dir="ltr"><font color="#000000" face="arial, helvetica, sans-serif"><a href="http://www.chem.rochester.edu/groups/huo/people/" target="_blank">http://www.chem.rochester.edu/<wbr>groups/huo/people/</a></font></div>
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                  <div class="gmail_quote">On Mon, Aug 1, 2016 at 5:01
                    PM, Ben Hourahine <span dir="ltr"><<a href="mailto:benjamin.hourahine@strath.ac.uk" target="_blank">benjamin.hourahine@strath.ac.<wbr>uk</a>></span>
                    wrote:<br>
                    <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hello
                      Sharma,<br>
                      <br>
                      the initial geometry in <a href="http://input.xyz" rel="noreferrer" target="_blank">input.xyz</a> does not seem to
                      have been optimised<br>
                      for the DFTB3 model. So one possibility is that it
                      is the energy stored<br>
                      in the structure coming out during the MD run.
                      I'll start it off from a<br>
                      relaxed geometry and see what happens.<br>
                      <br>
                      Regards<br>
                      <br>
                      Ben<br>
                      <div>
                        <div><br>
                          On 25/07/16 16:26, Sharma SRK Chaitanya
                          Yamijala wrote:<br>
                          > Dear DFTB members,<br>
                          ><br>
                          > I ran an NVT MD simulation (with
                          Nose-Hover thermostat) of a fullerene and<br>
                          > oligothiophene monomer with a 0.1 fs time
                          step and for a total simulation<br>
                          > time of 30 ps (attached file is for 3
                          ps). I observed that the molecules<br>
                          > are moving apart from each other after 2
                          ps or so. Similar simulation with<br>
                          > CP2K didn't show this behavior. Could you
                          please suggest any changes in my<br>
                          > input file to avoid this behavior?<br>
                          ><br>
                          > Thanking you,<br>
                          > Sincerely,<br>
                          > Sharma.<br>
                          ><br>
                          ><br>
                          >
                          ------------------------------<wbr>------------------------------<wbr>--------<br>
                          > Sharma<br>
                          > <a href="http://www.chem.rochester.edu/groups/huo/people/" rel="noreferrer" target="_blank">http://www.chem.rochester.edu/<wbr>groups/huo/people/</a><br>
                          ><br>
                          ><br>
                          ><br>
                        </div>
                      </div>
                      >
                      ______________________________<wbr>_________________<br>
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                      > <a href="mailto:DFTB-Plus-User@mailman.zfn.uni-bremen.de" target="_blank">DFTB-Plus-User@mailman.zfn.uni<wbr>-bremen.de</a><br>
                      > <a href="https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user" rel="noreferrer" target="_blank">https://mailman.zfn.uni-bremen<wbr>.de/cgi-bin/mailman/listinfo/d<wbr>ftb-plus-user</a><br>
                      ><br>
                      <br>
                      --<br>
                      <br>
                            Dr. B. Hourahine, SUPA, Department of
                      Physics,<br>
                          University of Strathclyde, John Anderson
                      Building,<br>
                                  107 Rottenrow, Glasgow G4 0NG, UK.<br>
                          <a href="tel:%2B44%20141%20548%202325" value="+441415482325" target="_blank">+44 141
                        548 2325</a>, <a href="mailto:benjamin.hourahine@strath.ac.uk" target="_blank">benjamin.hourahine@strath.ac.u<wbr>k</a><br>
                      <br>
                      2013/14 THE Awards Entrepreneurial University of
                      the Year<br>
                            2012/13 THE Awards UK University of the Year<br>
                      <br>
                         The University of Strathclyde is a charitable
                      body,<br>
                              registered in Scotland, number SC015263<br>
                      ______________________________<wbr>_________________<br>
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      <br>
      <pre>______________________________<wbr>_________________
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<a href="mailto:DFTB-Plus-User@mailman.zfn.uni-bremen.de" target="_blank">DFTB-Plus-User@mailman.zfn.uni<wbr>-bremen.de</a>
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    </blockquote>
    <br>
    </div></div><pre cols="72"><div><div>-- 
      Dr. B. Hourahine, SUPA, Department of Physics,
    University of Strathclyde, John Anderson Building,
            107 Rottenrow, Glasgow G4 0NG, UK.
    <a href="tel:%2B44%20141%20548%202325" value="+441415482325" target="_blank">+44 141 548 2325</a>, <a href="mailto:benjamin.hourahine@strath.ac.uk" target="_blank">benjamin.hourahine@strath.ac.u<wbr>k</a></div></div>

2013/4 THE Awards Entrepreneurial University of the Year
      2012/13 THE Awards UK University of the Year

   The University of Strathclyde is a charitable body,
        registered in Scotland, number SC015263</pre>
  </div>

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