<div dir="ltr">Dear Ben,<div><br></div><div>Okay. I will try to include the dispersion corrections and re-run it. I will send them directly to you.</div><div><br></div><div>Thanks,</div><div>Sharma.</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>
<br><div class="gmail_quote">On Thu, Aug 4, 2016 at 2:08 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">
  
    
  
  <div bgcolor="#FFFFFF" text="#000000">
    <p>Hello Sharma,</p>
    <p>we should probably move the discussion off list, but is this
      system perhaps bound together by dispersion interactions in the
      CP2K model you used? These are turned off for the dftb_in.hsd.<br>
    </p>
    Regards<span><font color="#888888"><br>
    <br>
    Ben</font></span><div><div><br>
    <br>
    <div>On 04/08/16 18:27, Sharma SRK Chaitanya
      Yamijala wrote:<br>
    </div>
    <blockquote type="cite">
      
      <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" target="_blank">https://drive.google.com/open?<wbr>id=0B7l7TJgy0hzhWmxEY1lodEdUdU<wbr>E</a><br>
        </div>
      </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 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">
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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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                  <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.un<wbr>i-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>
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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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                          <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>
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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>
                                    <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">
                                        <div bgcolor="#FFFFFF" text="#000000">
                                          <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>
                                                </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>
                                                      </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> <br>
                                                          <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>
                                                          >
                                                          DFTB-Plus-User
                                                          mailing list<br>
                                                          > <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>
                                                          DFTB-Plus-User
                                                          mailing list<br>
                                                          <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></blockquote>
                                                          </div>
                                                          <br>
                                                          </div>
                                                        </div>
                                                      </div>
                                                    </blockquote>
                                                  </div>
                                                  <br>
                                                </div>
                                                <br>
                                                <fieldset></fieldset>
                                                <br>
                                                <pre>______________________________<wbr>_________________
DFTB-Plus-User mailing list
<a href="mailto:DFTB-Plus-User@mailman.zfn.uni-bremen.de" target="_blank">DFTB-Plus-User@mailman.zfn.uni<wbr>-bremen.de</a>
<a href="https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user" target="_blank">https://mailman.zfn.uni-bremen<wbr>.de/cgi-bin/mailman/listinfo/d<wbr>ftb-plus-user</a></pre>
    </blockquote>
    

    </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>


______________________________<wbr>_________________

DFTB-Plus-User mailing list

<a href="mailto:DFTB-Plus-User@mailman.zfn.uni-bremen.de" target="_blank">DFTB-Plus-User@mailman.zfn.uni<wbr>-bremen.de</a>

<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>
</blockquote></div>
</div></div></div>
</blockquote></div>
</div></div></div>
</div>
</div></div></div>
</blockquote></div>
</div>


<fieldset></fieldset>
<pre>______________________________<wbr>_________________
DFTB-Plus-User mailing list
<a href="mailto:DFTB-Plus-User@mailman.zfn.uni-bremen.de" target="_blank">DFTB-Plus-User@mailman.zfn.uni<wbr>-bremen.de</a>
<a href="https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user" target="_blank">https://mailman.zfn.uni-bremen<wbr>.de/cgi-bin/mailman/listinfo/<wbr>dftb-plus-user</a></pre>

</blockquote>
<pre cols="72">-- 
      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>

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></div></div><br>______________________________<wbr>_________________<br>
DFTB-Plus-User mailing list<br>
<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/<wbr>dftb-plus-user</a><br></blockquote></div><br></div></div>