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    On 8/11/2011 3:17 AM, Steven Neumann wrote:
    <blockquote
cite="mid:CAKZJqQGpqWX_9OmEXfsu8qV-N1BOYbUwUnu5mZZ93=Wx7X1O3g@mail.gmail.com"
      type="cite"><br>
      <br>
      <div class="gmail_quote">On Mon, Nov 7, 2011 at 2:26 PM, Justin A.
        Lemkul <span dir="ltr">&lt;<a moz-do-not-send="true"
            href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>&gt;</span>
        wrote:<br>
        <blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px
          0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote"><br>
          <br>
          Steven Neumann wrote:<br>
          <blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px
            0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
            <div class="im">Dear Gmx Users,<br>
              &nbsp;I know that this problem has been discussed may times but
              I cannot find the solution to get rid of pbc in my system:
              protein and ligand. I followed the workflow:<br>
              &nbsp;<br>
              1. &nbsp; &nbsp; &nbsp;First make your molecules whole if you want them
              whole<br>
              <br>
              trjconv -f md.trr -s md.tpr -pbc whole -ur compact -o
              mdwhole.xtc<br>
              <br>
              2. &nbsp; &nbsp; &nbsp;Cluster your molecules/particles if you want them
              clustered<br>
              <br>
              3. &nbsp; &nbsp; &nbsp;Extract the first frame from the trajectory as
              reference for removing jumps if you want to remove jumps.<br>
              <br>
              trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb<br>
              <br>
              4. &nbsp; &nbsp; &nbsp;Remove jumps if you want to have them removed
              using the first frame<br>
              <br>
              trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o
              mdwholeNOjump.xtc<br>
              <br>
            </div>
            5. &nbsp; &nbsp; &nbsp;Center your system using some criterion. Doing so
            shifts the system, so don't use |trjconv -|pbc| nojump|
            after this step.
            <div class="im"><br>
              <br>
              trjconv -f mdwholeNOjump.xtc -center -o
              mdwholeNOjumpCENTER.xtc<br>
              <br>
              6. &nbsp; &nbsp; &nbsp;Put everything in some box.<br>
              <br>
              trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o
              mdwholeNOjumpCENTERbox.xtc<br>
              <br>
              7. &nbsp; &nbsp; &nbsp;Fit if desired and don't use any PBC related
              option afterwards.<br>
              <br>
              trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit
              rot+trans -o mdfinal.xtc<br>
              <br>
              &nbsp;<br>
              I used SYSTEM everywhere as output orinput. However, my
              ligand is still jumping like a fly around the stable
              protein. Do you have any suggestions?<br>
              <br>
              &nbsp;<br>
            </div>
          </blockquote>
          <br>
          Center on either the protein, the ligand, or some custom index
          group of residues surrounding the ligand. &nbsp;Centering on the
          whole system usually doesn't do anything useful.<br>
          <br>
          -Justin<br>
          <br>
        </blockquote>
        <div>&nbsp;</div>
        <div>Thank you guys but...</div>
        <div>&nbsp;</div>
        <div>I am trying and it does not work... my ligand is jumping
          like an idiot outside the box changing its position even two
          dimensions of box in one frame. </div>
      </div>
    </blockquote>
    <br>
    I have no idea what you mean by this.<br>
    <br>
    <blockquote
cite="mid:CAKZJqQGpqWX_9OmEXfsu8qV-N1BOYbUwUnu5mZZ93=Wx7X1O3g@mail.gmail.com"
      type="cite">
      <div class="gmail_quote">
        <div>I removed -ur compact from the first line and I tried
          centering on ligand or protein (centering group: LIG or
          Protein, output: SYSTEM). No results... </div>
        <div>My ligand at the begining of the simualtion is not within
          the protein. Please, help :(((( I tried this workflow with
          many ligands and same protein - it worked! Now it does not...</div>
      </div>
    </blockquote>
    <br>
    Sure. So far you've given us no understanding of what your ligand is
    doing during the simulation. If you don't know either, go and look
    at it. Then go and look at the trajectory from each stage of your
    work flow and see what it looks like and how things are changing.
    Then when something looks wrong you have a single step you can
    trouble shoot... maybe the operation is not sensible, maybe the way
    you did it is wrong, maybe the code is wrong.<br>
    <br>
    You cannot expect to transfer work flows from another simulation
    without considering what is happening in this one. Scenarios where
    your ligand is diffusing away from your protein and reassociating to
    another side require different work flows from one where the ligand
    stays nearby a binding pocket. In the latter, you should probably
    use -pbc cluster in step 2, though some of the time it won't matter.
    In the former, using -nojump to allow diffusion out of the box, and
    then step 6 to put everything back in the box doesn't make sense.
    Just doing operations and selecting groups without considering the
    nature of the operation will get a garbage result. There's a good
    reason mdrun doesn't attempt to second-guess how you would like all
    of this done!<br>
    <br>
    Mark<br>
    <br>
    <blockquote
cite="mid:CAKZJqQGpqWX_9OmEXfsu8qV-N1BOYbUwUnu5mZZ93=Wx7X1O3g@mail.gmail.com"
      type="cite">
      <div class="gmail_quote">
        <div>Here is my workflow:</div>
        <div>&nbsp;</div>
        <div>
          <p style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 54pt;
            mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;
            mso-list: l0 level1 lfo1; tab-stops: list 54.0pt"
            class="MsoNormal"><font face="Times New Roman"><span
                style="mso-list: Ignore"><font size="3">1.</font><span
                  style="FONT: 7pt 'Times New Roman'">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><font
                size="3">First make your molecules whole if you want
                them whole.</font></font></p>
          <p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto;
            mso-margin-bottom-alt: auto" class="MsoNormal"><span
              style="COLOR: red"><font size="3"><font face="Times New
                  Roman">trjconv -f md.trr -s md.tpr -pbc whole -o
                  mdwhole.xtc</font></font></span></p>
          <p style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 54pt;
            mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;
            mso-list: l0 level1 lfo1; tab-stops: list 54.0pt"
            class="MsoNormal"><font face="Times New Roman"><span
                style="mso-list: Ignore"><font size="3">2.</font><span
                  style="FONT: 7pt 'Times New Roman'">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><font
                size="3">Cluster your molecules/particles if you want
                them clustered</font></font></p>
          <p style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 54pt;
            mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;
            mso-list: l0 level1 lfo1; tab-stops: list 54.0pt"
            class="MsoNormal"><font face="Times New Roman"><span
                style="mso-list: Ignore"><font size="3">3.</font><span
                  style="FONT: 7pt 'Times New Roman'">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><font
                size="3">Extract the first frame from the trajectory as
                reference for removing jumps if you want to remove
                jumps.</font></font></p>
          <p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto;
            mso-margin-bottom-alt: auto" class="MsoNormal"><span
              style="COLOR: red"><font size="3"><font face="Times New
                  Roman">trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o
                  1stframe.pdb</font></font></span></p>
          <p style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 54pt;
            mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;
            mso-list: l0 level1 lfo1; tab-stops: list 54.0pt"
            class="MsoNormal"><font face="Times New Roman"><span
                style="mso-list: Ignore"><font size="3">4.</font><span
                  style="FONT: 7pt 'Times New Roman'">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><font
                size="3">Remove jumps if you want to have them removed
                using the first frame (system)</font></font></p>
          <p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto;
            mso-margin-bottom-alt: auto" class="MsoNormal"><span
              style="COLOR: red"><font size="3"><font face="Times New
                  Roman">trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc
                  nojump -o mdwholeNOjump.xtc</font></font></span></p>
          <p style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 54pt;
            mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;
            mso-list: l0 level1 lfo1; tab-stops: list 54.0pt"
            class="MsoNormal"><font face="Times New Roman"><span
                style="mso-list: Ignore"><font size="3">5.</font><span
                  style="FONT: 7pt 'Times New Roman'">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><font
                size="3">Center your system using some criterion. Doing
                so shifts the system, so don't use </font></font><code><span
                style="FONT-SIZE: 10pt">trjconv -</span></code><span
              class="highlight"><span style="BACKGROUND: yellow"><font
                  face="Times New Roman" size="3">pbc</font></span></span><code><span
                style="FONT-SIZE: 10pt"> nojump</span></code><font
              face="Times New Roman" size="3"> after this step (tried
              centering on LIG or PROTEIN)</font></p>
          <p style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 54pt;
            mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;
            mso-list: l0 level1 lfo1; tab-stops: list 54.0pt"
            class="MsoNormal"><span style="COLOR: red"><font size="3"><font
                  face="Times New Roman">trjconv -f mdwholeNOjump.xtc -n
                  Ligand.ndx -center -o mdwholeNOjumpCENTER.xtc</font></font></span></p>
          <p style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 54pt;
            mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;
            mso-list: l0 level1 lfo1; tab-stops: list 54.0pt"
            class="MsoNormal"><font face="Times New Roman"><span
                style="mso-list: Ignore"><font size="3">6.</font><span
                  style="FONT: 7pt 'Times New Roman'">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><font
                size="3">Put everything in some box.</font></font></p>
          <p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto;
            mso-margin-bottom-alt: auto" class="MsoNormal"><span
              style="COLOR: red"><font size="3"><font face="Times New
                  Roman">trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6
                  -o mdwholeNOjumpCENTERbox.xtc</font></font></span></p>
          <p style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 54pt;
            mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;
            mso-list: l0 level1 lfo1; tab-stops: list 54.0pt"
            class="MsoNormal"><font face="Times New Roman"><span
                style="mso-list: Ignore"><font size="3">7.</font><span
                  style="FONT: 7pt 'Times New Roman'">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><font
                size="3">Fit if desired and don't use any <span
                  class="highlight"><span style="BACKGROUND: yellow">PBC</span></span>
                related option afterwards.</font></font></p>
          <p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto;
            mso-margin-bottom-alt: auto" class="MsoNormal"><span
              style="COLOR: red"><font size="3"><font face="Times New
                  Roman">trjconv -f mdwholeNOjumpCENTERbox.xtc -s
                  1stframe.pdb -fit rot+trans -o mdfinal.xtc</font></font></span></p>
          <span style="FONT-FAMILY: 'Times New Roman'; FONT-SIZE: 12pt;
            mso-fareast-font-family: 'Times New Roman';
            mso-ansi-language: EN-GB; mso-fareast-language: EN-GB;
            mso-bidi-language: AR-SA">With point three, the issue is
            that <a moz-do-not-send="true" title="Documentation/Gromacs
              Utilities/trjconv"
              href="http://www.gromacs.org/Documentation/Gromacs_Utilities/trjconv">trjconv</a>
            removes the jumps from the first frame using the reference
            structure provided with </span><code><span
              style="FONT-SIZE: 10pt; mso-ansi-language: EN-GB;
              mso-fareast-language: EN-GB; mso-bidi-language: AR-SA">-s</span></code><span
            style="FONT-FAMILY: 'Times New Roman'; FONT-SIZE: 12pt;
            mso-fareast-font-family: 'Times New Roman';
            mso-ansi-language: EN-GB; mso-fareast-language: EN-GB;
            mso-bidi-language: AR-SA">. If the reference structure (run
            input file) is not clustered/whole, </span><code><span
              style="FONT-SIZE: 10pt; mso-ansi-language: EN-GB;
              mso-fareast-language: EN-GB; mso-bidi-language: AR-SA">trjconv
              -</span></code><span class="highlight"><span
              style="FONT-FAMILY: 'Times New Roman'; BACKGROUND: yellow;
              FONT-SIZE: 12pt; mso-fareast-font-family: 'Times New
              Roman'; mso-ansi-language: EN-GB; mso-fareast-language:
              EN-GB; mso-bidi-language: AR-SA">pbc</span></span><code><span
              style="FONT-SIZE: 10pt; mso-ansi-language: EN-GB;
              mso-fareast-language: EN-GB; mso-bidi-language: AR-SA">
              nojump</span></code><span style="FONT-FAMILY: 'Times New
            Roman'; FONT-SIZE: 12pt; mso-fareast-font-family: 'Times New
            Roman'; mso-ansi-language: EN-GB; mso-fareast-language:
            EN-GB; mso-bidi-language: AR-SA"> will undo steps 1 and</span></div>
        <div>&nbsp;</div>
        <div>Steven</div>
        <div>&nbsp;</div>
        <div>&nbsp;</div>
        <div>========================================<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]<a moz-do-not-send="true" href="http://vt.edu/"
            target="_blank">vt.edu</a> | <a moz-do-not-send="true"
            href="tel:%28540%29%20231-9080" target="_blank"
            value="+15402319080">(540) 231-9080</a><br>
          <a moz-do-not-send="true"
            href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
            target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
          <br>
          ======================================== </div>
        <blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px
          0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
          <div>
            <div class="h5"><br>
              -- <br>
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                href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
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        </blockquote>
      </div>
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