<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div id="yiv2074674631"><div><div style="color: rgb(0, 0, 0); font-family: times new roman, new york, times, serif; font-size: 12pt; background-color: rgb(255, 255, 255);"><div id="yiv2074674631yui_3_2_0_17_133358881838643"><span id="yiv2074674631yui_3_2_0_17_133358881838679">Dear All,</span></div><div><span id="yiv2074674631yui_3_2_0_17_133358881838686"></span>&nbsp;</div><div><span id="yiv2074674631yui_3_2_0_17_1333588818386171">According to "http://www.gromacs.org/Documentation/How-tos/Extending_Simulations"&nbsp;, the commands for extending MD are:</span></div><div><span></span>&nbsp;</div><div><span></span>&nbsp;</div><div>tpbconv -s previous.tpr -extend timetoextendby -o next.tpr<br>mdrun -s next.tpr -cpi previous.cpt</div><div>&nbsp;</div><div>But if you read
 "http://www.gromacs.org/Documentation/File_Formats/Checkpoint_File", it suggest for extension of MD, state.cpt should be used. But if we use state.cpt for extension, in</div><div>&nbsp;</div><div>"</div><div>tpbconv -s previous.tpr -extend timetoextendby -o next.tpr<br>mdrun -s next.tpr -cpi previous.cpt</div><div>"</div><div>&nbsp;</div><div>the "previous" in previous.tpr in tpbconv will be conflicting with "previous" in previous.cpt in mdrun.</div><div>&nbsp;</div><div>In addition in command</div><div>"</div><div>trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact</div><div>"</div><div>&nbsp;</div><div>can we change md_0_1.xtc to traj.xtc?</div><div>&nbsp;</div><div>I am looking forward to getting a clarification from you.</div><div>&nbsp;</div><div>Cheers,</div><div>&nbsp;</div><div>Acoot<var id="yui-ie-cursor"></var></div><div><br>&nbsp;</div><div><br id="yiv2074674631yui_3_2_0_17_133358881838645"></div>  <div
 style="font-family: times new roman, new york, times, serif; font-size: 12pt;" id="yiv2074674631yui_3_2_0_17_133358881838649" class="yiv2074674631ms__id2257"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;" class="yiv2074674631ms__id2259"> <div dir="ltr"> <font size="2" face="Arial"> <div style="margin: 5px 0px; padding: 0px; border: 1px solid rgb(204, 204, 204); height: 0px; line-height: 0; font-size: 0px;" class="yiv2074674631hr yiv2074674631yui-non yiv2074674631yui-skip"></div>  <b><span style="font-weight: bold;">From:</span></b> Mark Abraham &lt;Mark.Abraham@anu.edu.au&gt;<br> <b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users &lt;gmx-users@gromacs.org&gt; <br> <b><span style="font-weight: bold;">Sent:</span></b> Wednesday, 4 April 2012 6:56 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] the -extend function of the tpbconv command<br> </font>
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    On 4/04/2012 6:24 PM, Acoot Brett wrote:
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        <div><span>Hi Justin and All,</span></div>
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                  <div><span></span>&nbsp;</div>
                  <div><span>The on-line document on "<font style="background-color: rgb(255, 255, 0);">Exten</font>ding
                      Simulations" writes,</span></div>
                  <div><span></span>&nbsp;</div>
                  <div><span>"You might want to use the <span style="font-family: courier new, courier, monospace;" class="yiv2074674631ms__id2270">-append</span> option of <a title="Documentation/Gromacs_Utilities/mdrun" href="http://www.gromacs.org/Documentation/Gromacs_Utilities/mdrun" rel="nofollow" target="_blank"><font color="#0066cc">mdrun</font></a> to append the
                      new output to the old files. Note that this will
                      only work when the old output files have not been
                      modified by the user. Appending is the default
                      behavior as of version 4.5."</span></div>
                  <div><span></span>&nbsp;</div>
                  <div><span>We can see "Appending is the default
                      behavior as of version 4.5", and what I use is
                      version 4.5. Thus for mdrun, even without mention
                      "<span style="font-family: courier new, courier, monospace;" class="yiv2074674631ms__id2271">-append</span> " appending should be
                      automatically done.</span></div>
                  <div><span></span>&nbsp;</div>
                  <div><span>In addition, after the old output files
                      were created, I only use the "trjconv" to process
                      them, and I did not modify them.</span></div>
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    <br>
    Any change is enough to prevent appending. mdrun computed a checksum
    when it wrote them, saved the checksums in the checkpoint file, and
    demands that newly-computed ones match when attempting to append
    later. Use only the original trajectory files when attempting to
    append.<br>
    <br>
    Mark<br>
    <br>
    <blockquote type="cite">
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                  <div><span></span>&nbsp;</div>
                  <div><span>Thus the reason why the extended part
                      output files were not automatically appended to my
                      original old outputfiles according to what I have
                      done (tpbconv -s previous.tpr -extend
                      timetoextendby -o next.tpr&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; mdrun -s next.tpr
                      -cpi previous.cpt)<var id="yiv2074674631yui-ie-cursor"></var> is still
                      unclear.</span></div>
                  <div><span></span>&nbsp;</div>
                  <div><span>Will you please give an explaination?</span></div>
                  <div><span></span>&nbsp;</div>
                  <div><span>Cheers,</span></div>
                  <div><span></span>&nbsp;</div>
                  <div><span>Acoot</span></div>
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                      <div dir="ltr"> <font size="2" face="Arial"> <b><span style="font-weight: bold;">From:</span></b>
                          Justin A. Lemkul <a class="yiv2074674631moz-txt-link-rfc2396E" href="mailto:jalemkul@vt.edu" rel="nofollow" target="_blank" ymailto="mailto:jalemkul@vt.edu">&lt;jalemkul@vt.edu&gt;</a><br>
                          <b><span style="font-weight: bold;">To:</span></b>
                          Acoot Brett <a class="yiv2074674631moz-txt-link-rfc2396E" href="mailto:acootbrett@yahoo.com" rel="nofollow" target="_blank" ymailto="mailto:acootbrett@yahoo.com">&lt;acootbrett@yahoo.com&gt;</a>;
                          Discussion list for GROMACS users
                          <a class="yiv2074674631moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org" rel="nofollow" target="_blank" ymailto="mailto:gmx-users@gromacs.org">&lt;gmx-users@gromacs.org&gt;</a> <br>
                          <b><span style="font-weight: bold;">Sent:</span></b>
                          Wednesday, 4 April 2012 10:36 AM<br>
                          <b><span style="font-weight: bold;">Subject:</span></b>
                          Re: [gmx-users] the -extend function of the
                          tpbconv command<br>
                        </font> </div>
                      <br>
                      <br>
                      <br>
                      Acoot Brett wrote:<br>
                      &gt; Dear All,<br>
                      &gt;&nbsp; I have completed a 1ns production MD. Then I
                      intended to extend it for another 1 ns.<br>
                      &gt;&nbsp; I use command<br>
                      &gt;&nbsp; "tpbconv -s previous.tpr -extend
                      timetoextendby -o next.tpr<br>
                      &gt; mdrun -s next.tpr -cpi previous.cpt"<br>
                      &gt;&nbsp; I think the results will be automatically
                      attended to previous md_0_1.tpr and
                      md_0_1_noPBC.xtc.<br>
                      &gt;&nbsp; <br>
                      <br>
                      Only if you then run mdrun -append and the files
                      are appended.&nbsp; tpbconv doesn't do any of this for
                      you, it just creates a new run input file capable
                      of running a longer simulation.&nbsp; The fact that you
                      have a file called "md_0_1_noPBC.xtc" seems like
                      you've manipulated it in some way, so you
                      shouldn't (and likely can't) append to it.&nbsp; You
                      should append to your original files.<br>
                      <br>
                      &gt; Then I use "g_rms -s md_0_1.tpr -f
                      md_0_1_noPBC.xtc -o rmsd.xvg -tu ns" to get the
                      rmsd.xvg file. Then I use "xmgrace -nxy
                      potential.xvg" to display it. However I find for
                      the&nbsp; curve the x-axis is from 0 ns to 1 ns, not
                      from 0 ns to 2 ns.<br>
                      &gt;&nbsp; <br>
                      <br>
                      If you haven't run a new simulation, you'll only
                      have the data that already exists.<br>
                      <br>
                      &gt; The definition of "-extend" of the command
                      "tpbconv" is "Extend runtime by this amount (ps)".
                      Thus the commands I used are correct.<br>
                      &gt;&nbsp; <br>
                      <br>
                      You haven't shown us your actual tpbconv command,
                      so there's no way to verify that.&nbsp; In any case,
                      tpbconv doesn't actually extend the simulation,
                      mdrun does.<br>
                      <br>
                      &gt; Will you please tell me how to process for
                      the extension MD so that the curve of the rmsd.xvg
                      (and all the other xvg files) will have x-axis
                      from the 0 to the 2 ns (2 ns is the total MD time,
                      including the 1 ns extended part)?<br>
                      &gt;&nbsp; <br>
                      <br>
                      There are two steps here:<br>
                      <br>
                      <a href="http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Version_4" rel="nofollow" target="_blank">http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Version_4</a><br>
                      <br>
                      You need to do both.<br>
                      <br>
                      -Justin<br>
                      <br>
                      -- ========================================<br>
                      <br>
                      Justin A. Lemkul<br>
                      Ph.D. Candidate<br>
                      ICTAS Doctoral Scholar<br>
                      MILES-IGERT Trainee<br>
                      Department of Biochemistry<br>
                      Virginia Tech<br>
                      Blacksburg, VA<br>
                      jalemkul[at]vt.edu | (540) 231-9080<br>
                      <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" rel="nofollow" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
                      <br>
                      ========================================<br>
                      <br>
                      <br>
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</div><br>-- <br>gmx-users mailing list&nbsp; &nbsp; <a href="mailto:gmx-users@gromacs.org" rel="nofollow" target="_blank" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" rel="nofollow" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" rel="nofollow" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" rel="nofollow" target="_blank" ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" rel="nofollow" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br><br> </div>
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