<div dir="ltr">Hi Tianwu,<div style>just to be sure, can you try to compile with CMAKE_BUILD_TYPE=Debug</div><div style>and repeating again the runs?</div><div style><br></div><div style>Francesco</div></div><div class="gmail_extra">
<br><br><div class="gmail_quote">2013/6/13 Mark Abraham <span dir="ltr">&lt;<a href="mailto:mark.j.abraham@gmail.com" target="_blank">mark.j.abraham@gmail.com</a>&gt;</span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr"><br><div class="gmail_extra"><br><br><div class="gmail_quote"><div class="im">On Wed, Jun 12, 2013 at 10:58 PM, Tianwu Zang <span dir="ltr">&lt;<a href="mailto:tz4@rice.edu" target="_blank">tz4@rice.edu</a>&gt;</span> wrote:<br>

<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi all,<div>I am using a very common system for testing, with only one protein (~1000+ atoms) and ~7000+ water atoms with box size = 4.5</div>

<div>When I tried rerun the simulation, results kept the same with the last run for the same kernel, but became quite different (even at step=0) for different kernel, like using generic kernel in the first run and specific kernel in the second run..</div>


<div>In my case, for specific kernel, f[0]~884 and for generic kernel f[0]~337, which is a huge difference..</div><div>I have already set the variable gen_seed in my .mdp file so there shouldn&#39;t be any problem of random seed.</div>


<div>Now I am wondering if these force results should not differ from each other, where I am doing wrong?</div></div></blockquote><div><br></div></div><div>OK. What&#39;s your .mdp file?</div><span class="HOEnZb"><font color="#888888"><div>
<br></div><div>
Mark</div></font></span><div><div class="h5"><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>Thanks again,</div><div>-Mark</div></div>
<div><div>
<div class="gmail_extra"><br><br><div class="gmail_quote">
On Wed, Jun 12, 2013 at 8:05 AM, francesco oteri <span dir="ltr">&lt;<a href="mailto:francesco.oteri@gmail.com" target="_blank">francesco.oteri@gmail.com</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">


<div dir="ltr">Hi,<div>Marc said it is using -rerun and, as far as I know and basing on my experience, </div><div>it gives exactly the same reults. Of course, also the seed has to be the same :D</div><span><font color="#888888"><div>



<br></div><div>Francesco</div></font></span></div><div><div><div class="gmail_extra"><br><br><div class="gmail_quote">2013/6/12 Berk Hess <span dir="ltr">&lt;<a href="mailto:hess@kth.se" target="_blank">hess@kth.se</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>Hi,<br>
      <br>
      You haven&#39;t said at what step this happens.<br>
      At step zero the forces should match, except for the last
      decimal(s).<br>
      But since MD is chaotic, trajectories diverge exponentially, which
      is very fast.<br>
      This usually means forces are significantly decorrelated after 100
      to 1000 steps.<br>
      <br>
      Cheers,<br>
      <br>
      Berk<div><div><br>
      <br>
      On 06/12/2013 01:50 PM, Mark Abraham wrote:<br>
    </div></div></div><div><div>
    <blockquote type="cite">
      
      <div dir="ltr"><br>
        <div class="gmail_extra"><br>
          <br>
          <div class="gmail_quote">On Wed, Jun 12, 2013 at 3:28 AM, Mark
            Tianwu Zang <span dir="ltr">&lt;<a href="mailto:zangtw@gmail.com" target="_blank">zangtw@gmail.com</a>&gt;</span>
            wrote:<br>
            <blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
              <div dir="ltr"><span style="font-family:arial,sans-serif;font-size:13px">Hi
                  Francesco and Mark,</span>
                <div style="font-family:arial,sans-serif;font-size:13px">
                  Thanks for your precious advice. Now this time I
                  didn&#39;t insert any code but use the .mdp options
                  instead. I used the following steps: first set the
                  environment variable GMX_NB_GENERIC=1, run the
                  GROMACS, and run again with the same input but
                  GMX_NB_GENERIC unset. Next, compare two force.xvg
                  generated from two traj.trr using g_traj. However, I
                  still found the results different from each other.. My
                  gcc version is 4.6.3(almost the newest), my fftw
                  version is 3.3.3(double precision, and GROMACS is also
                  build in double-precision) and I use the argument
                  --reprod to make sure the calculation of PME is
                  reproducible. </div>
                <div style="font-family:arial,sans-serif;font-size:13px">My
                  running command for GROMACS is</div>
                <div style="font-family:arial,sans-serif;font-size:13px">mpirun
                  -np 2 mdrun_mpi -s test.tpr -v -reprod</div>
              </div>
            </blockquote>
            <div><br>
            </div>
            <div>That&#39;s better, but the advice here is worth
              following: <a href="http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy" target="_blank">http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy</a></div>
            <div> </div>
            <blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
              <div dir="ltr">
                <div style="font-family:arial,sans-serif;font-size:13px">
                  I tried to attach my test tpr and mdp file in this
                  email but my attempt was not approved by administrator
                  because the email would be oversized..</div>
              </div>
            </blockquote>
            <div><br>
            </div>
            <div>Describing in words what your system is doing
              would be a good start ;-)</div>
            <div><br>
            </div>
            <div>Mark</div>
            <div><br>
            </div>
            <blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
              <div dir="ltr">
                <span><font color="#888888">
                    <div style="font-family:arial,sans-serif;font-size:13px"><br>
                    </div>
                    <div style="font-family:arial,sans-serif;font-size:13px">
                      -Mark</div>
                  </font></span></div>
              <div>
                <div>
                  <div class="gmail_extra"><br>
                    <br>
                    <div class="gmail_quote">On Sat, Jun 8, 2013 at 7:25
                      AM, francesco oteri <span dir="ltr">&lt;<a href="mailto:francesco.oteri@gmail.com" target="_blank">francesco.oteri@gmail.com</a>&gt;</span>
                      wrote:<br>
                      <blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
                        <div dir="ltr">In my case the excuse was that
                          the system administrator never updated the
                          compiler. 
                          <div>
                            So I after a couple of days I installed the
                            new compiler.</div>
                          <div>In any case, I noticed that the
                            problem disappeared using the &quot;Debug&quot;
                            version so  I guess </div>
                          <div>it is something related either to the
                            optimized kernel or the optimization
                            strategy used by the compiler. </div>
                          <span><font color="#888888">
                              <div><br>
                              </div>
                              <div><br>
                              </div>
                              <div>Francesco</div>
                            </font></span></div>
                        <div>
                          <div>
                            <div class="gmail_extra">
                              <br>
                              <br>
                              <div class="gmail_quote">2013/6/8 Mark
                                Abraham <span dir="ltr">&lt;<a href="mailto:mark.j.abraham@gmail.com" target="_blank">mark.j.abraham@gmail.com</a>&gt;</span><br>
                                <blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
                                  <div dir="ltr"><br>
                                    <div class="gmail_extra"><br>
                                      <br>
                                      <div class="gmail_quote">
                                        <div>On Sat, Jun 8, 2013 at
                                          12:59 PM, francesco oteri <span dir="ltr">&lt;<a href="mailto:francesco.oteri@gmail.com" target="_blank">francesco.oteri@gmail.com</a>&gt;</span>
                                          wrote:<br>
                                          <blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
                                            <div dir="ltr">H Mark,
                                              <div>I had a similar
                                                problem recently and,
                                                eventually, I figured
                                                out the cause was the
                                                compiler version.</div>
                                              <div>I was using gcc4.1
                                                and my problem got
                                                solved using a more
                                                recent version.
                                                Actually, this issue </div>
                                              <div>in the website is
                                                clearly stated. So,
                                                which compiler are you
                                                using?</div>
                                              <div>Could you report an
                                                example
                                                of inconsistency?</div>
                                            </div>
                                          </blockquote>
                                          <div><br>
                                          </div>
                                        </div>
                                        <div>That warning has been there
                                          many years, but AFAIK nobody
                                          ever identified the real
                                          problem (if it exists).
                                          Nevertheless, there is no
                                          excuse for using both GROMACS
                                          and such an old compiler! :-)</div>
                                        <span><font color="#888888">
                                            <div><br>
                                            </div>
                                            <div>Mark</div>
                                          </font></span>
                                        <div>
                                          <div>
                                            <div><br>
                                            </div>
                                            <blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
                                              <div dir="ltr">
                                                <div><br>
                                                </div>
                                                <div>Francesco </div>
                                              </div>
                                              <div class="gmail_extra">
                                                <div>
                                                  <div>
                                                    <br>
                                                    <br>
                                                    <div class="gmail_quote">2013/6/8
                                                      Mark Abraham <span dir="ltr">&lt;<a href="mailto:mark.j.abraham@gmail.com" target="_blank">mark.j.abraham@gmail.com</a>&gt;</span><br>
                                                      <blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
                                                        <div dir="ltr"><br>
                                                          <div class="gmail_extra"><br>
                                                          <br>
                                                          <div class="gmail_quote">On
                                                          Sat, Jun 8,
                                                          2013 at 1:44
                                                          AM, Mark
                                                          Tianwu Zang <span dir="ltr">&lt;<a href="mailto:zangtw@gmail.com" target="_blank">zangtw@gmail.com</a>&gt;</span>
                                                          wrote:<br>
                                                          <blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">




                                                          <div dir="ltr">Dear
                                                          all,
                                                          <div>I have
                                                          inserted only
                                                          a few lines
                                                          after update()
                                                          in md.c to
                                                          monitor how
                                                          forces change
                                                          after every
                                                          step. My codes
                                                          are very
                                                          simple, just
                                                          like:</div>
                                                          <div> </div>
                                                          <div>for i=0
                                                          to
                                                          md-&gt;nalloc</div>
                                                          <div>
                                                          <div> fprintf
                                                          f[i][0],
                                                          f[i][1],
                                                          f[i][2]</div>
                                                          </div>
                                                          </div>
                                                          </blockquote>
                                                          <div><br>
                                                          </div>
                                                          <div>That
                                                          seems like the
                                                          hard way to do
                                                          it, with
                                                          nstfout
                                                          available in
                                                          the .mdp
                                                          file. </div>
                                                          <div><br>
                                                          </div>
                                                          <blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">




                                                          <div dir="ltr">
                                                          <div>
                                                          <div>However,
                                                          I found the
                                                          results of my
                                                          output become
                                                          quite
                                                          different
                                                          after
                                                          exporting
                                                          GMX_NB_GENERIC=1,
                                                          which means
                                                          the forces
                                                          calculated by
                                                          generic kernel
                                                          and
                                                          interaction-specific
                                                          kernel are not
                                                          the same. I am
                                                          a little
                                                          confused now..
                                                          It this
                                                          phenomena
                                                          quite normal
                                                          or I ignored
                                                          something
                                                          important?</div>
                                                          </div>
                                                          </div>
                                                          </blockquote>
                                                          <div><br>
                                                          </div>
                                                          <div>AFAIK the
                                                          generic kernel
                                                          should serve
                                                          as a reference
                                                          for the
                                                          interaction-specific
                                                          kernels. If
                                                          not, there
                                                          might a
                                                          problem to
                                                          fix. Hard to
                                                          say without
                                                          context.</div>
                                                          <div><br>
                                                          </div>
                                                          <div>Mark</div>
                                                          <div><br>
                                                          </div>
                                                          <blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">




                                                          <div dir="ltr">
                                                          <div>
                                                          <div>Thanks a
                                                          lot!</div>
                                                          <span><font color="#888888">
                                                          <div>-Mark</div>
                                                          <div><br>
                                                          </div>
                                                          </font></span></div>
                                                          <div><br>
                                                          </div>
                                                          </div>
                                                          <span><font color="#888888">
                                                          <br>
                                                          --<br>
                                                          gmx-developers
                                                          mailing list<br>
                                                          <a href="mailto:gmx-developers@gromacs.org" target="_blank">gmx-developers@gromacs.org</a><br>
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                                                          </font></span></blockquote>
                                                          </div>
                                                          <br>
                                                          </div>
                                                        </div>
                                                        <br>
                                                        --<br>
                                                        gmx-developers
                                                        mailing list<br>
                                                        <a href="mailto:gmx-developers@gromacs.org" target="_blank">gmx-developers@gromacs.org</a><br>
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                                                        Please don&#39;t
                                                        post
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                                                        requests to the
                                                        list. Use the<br>
                                                        www interface or
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                                                      </blockquote>
                                                    </div>
                                                    <br>
                                                    <br clear="all">
                                                    <div><br>
                                                    </div>
                                                  </div>
                                                </div>
                                                <span><font color="#888888">-- <br>
                                                    Cordiali saluti,
                                                    Dr.Oteri Francesco
                                                  </font></span></div>
                                              <br>
                                              --<br>
                                              gmx-developers mailing
                                              list<br>
                                              <a href="mailto:gmx-developers@gromacs.org" target="_blank">gmx-developers@gromacs.org</a><br>
                                              <a href="http://lists.gromacs.org/mailman/listinfo/gmx-developers" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-developers</a><br>
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                                            </blockquote>
                                          </div>
                                        </div>
                                      </div>
                                      <br>
                                    </div>
                                  </div>
                                  <br>
                                  --<br>
                                  gmx-developers mailing list<br>
                                  <a href="mailto:gmx-developers@gromacs.org" target="_blank">gmx-developers@gromacs.org</a><br>
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                                  Please don&#39;t post (un)subscribe
                                  requests to the list. Use the<br>
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                                </blockquote>
                              </div>
                              <br>
                              <br clear="all">
                              <div><br>
                              </div>
                              -- <br>
                              Cordiali saluti, Dr.Oteri Francesco
                            </div>
                          </div>
                        </div>
                        <br>
                        --<br>
                        gmx-developers mailing list<br>
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                        list. Use the<br>
                        www interface or send it to <a href="mailto:gmx-developers-request@gromacs.org" target="_blank">gmx-developers-request@gromacs.org</a>.<br>
                      </blockquote>
                    </div>
                    <br>
                  </div>
                </div>
              </div>
              <br>
              --<br>
              gmx-developers mailing list<br>
              <a href="mailto:gmx-developers@gromacs.org" target="_blank">gmx-developers@gromacs.org</a><br>
              <a href="http://lists.gromacs.org/mailman/listinfo/gmx-developers" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-developers</a><br>
              Please don&#39;t post (un)subscribe requests to the list. Use
              the<br>
              www interface or send it to <a href="mailto:gmx-developers-request@gromacs.org" target="_blank">gmx-developers-request@gromacs.org</a>.<br>
            </blockquote>
          </div>
          <br>
        </div>
      </div>
      <br>
      <fieldset></fieldset>
      <br>
    </blockquote>
    <br>
  </div></div></div>

<br>--<br>
gmx-developers mailing list<br>
<a href="mailto:gmx-developers@gromacs.org" target="_blank">gmx-developers@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-developers" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-developers</a><br>
Please don&#39;t post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-developers-request@gromacs.org" target="_blank">gmx-developers-request@gromacs.org</a>.<br></blockquote></div><br><br clear="all"><div><br></div>-- <br>Cordiali saluti, Dr.Oteri Francesco
</div>
</div></div><br>--<br>
gmx-developers mailing list<br>
<a href="mailto:gmx-developers@gromacs.org" target="_blank">gmx-developers@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-developers" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-developers</a><br>
Please don&#39;t post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-developers-request@gromacs.org" target="_blank">gmx-developers-request@gromacs.org</a>.<br></blockquote></div><br></div>
</div></div><br>--<br>
gmx-developers mailing list<br>
<a href="mailto:gmx-developers@gromacs.org" target="_blank">gmx-developers@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-developers" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-developers</a><br>
Please don&#39;t post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-developers-request@gromacs.org" target="_blank">gmx-developers-request@gromacs.org</a>.<br></blockquote></div></div></div><br></div></div>
<br>--<br>
gmx-developers mailing list<br>
<a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-developers" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-developers</a><br>
Please don&#39;t post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@gromacs.org</a>.<br></blockquote></div><br><br clear="all"><div><br></div>-- <br>Cordiali saluti, Dr.Oteri Francesco
</div>