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    <div class="moz-cite-prefix">But you didn't write which interactions
      you want to exclude exactly. You write about groups, but that is
      incorrect, interactions contribute to the virial, not atoms.<br>
      I assume you want to exclude the solid-solid interactions. That
      can be done by setting all solid-solid interaction parameters to
      zero, assuming there are no charges. If there are charges, you can
      use the old group cutoff-scheme with energy group exclusions.<br>
      You write about solid-liquid interactions, but excluding those
      would not result in a meaningful virial, I would think.<br>
      <br>
      Berk<br>
      <br>
      On 06/25/2015 05:15 PM, Hardy, Adam wrote:<br>
    </div>
    <blockquote cite="mid:D1B1D91D.6B89%25ah259@hw.ac.uk" type="cite">
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          <div>If we were able to make the changes we want then the
            viral would be correct for what we need it for</div>
          <div><br>
          </div>
          <div>We applied the freezing over restraints because the
            restraints make other calculations substantially more
            difficult but we might have to revisit that train of
            thought.</div>
          <div><br>
          </div>
          <div>Adam</div>
          <div>
            <div>----------------------------------------------------------</div>
            <div>Adam Hardy</div>
            <div>PhD Student</div>
            <div>School of Engineering and Physical Sciences</div>
            <div>Heriot Watt University</div>
            <div>Edinburgh, EH14 4AS</div>
            <div>Phone: +441314513074</div>
            <div><a class="moz-txt-link-abbreviated" href="mailto:ah259@hw.ac.uk">ah259@hw.ac.uk</a></div>
            <div>----------------------------------------------------------</div>
          </div>
        </div>
      </div>
      <div><br>
      </div>
      <span id="OLK_SRC_BODY_SECTION">
        <div style="font-family:Calibri; font-size:11pt;
          text-align:left; color:black; BORDER-BOTTOM: medium none;
          BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT:
          0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid;
          BORDER-RIGHT: medium none; PADDING-TOP: 3pt">
          <span style="font-weight:bold">From: </span>&lt;<a
            moz-do-not-send="true"
            href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se">gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</a>&gt;
          on behalf of Berk Hess &lt;<a moz-do-not-send="true"
            href="mailto:hess@kth.se">hess@kth.se</a>&gt;<br>
          <span style="font-weight:bold">Reply-To: </span>"<a
            moz-do-not-send="true"
            href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>"
          &lt;<a moz-do-not-send="true"
            href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>&gt;<br>
          <span style="font-weight:bold">Date: </span>Thursday, 25 June
          2015 16:12<br>
          <span style="font-weight:bold">To: </span>"<a
            moz-do-not-send="true"
            href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>"
          &lt;<a moz-do-not-send="true"
            href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>&gt;<br>
          <span style="font-weight:bold">Subject: </span>Re:
          [gmx-developers] Modifying the shifted part of the viral<br>
        </div>
        <div><br>
        </div>
        <div>
          <div bgcolor="#FFFFFF" text="#000000">
            <div class="moz-cite-prefix">Hi,<br>
              <br>
              This can not be achieved easily.<br>
              But in most cases the virial becomes meaningless when you
              freeze particles.<br>
              You might get meaningful results when you use (tight)
              position restraints instead. Then you even have the option
              to scale the COM of a tube along with pressure scaling, if
              you want.<br>
              <br>
              Cheers,<br>
              <br>
              Berk<br>
              <br>
              On 06/25/2015 04:53 PM, Hardy, Adam wrote:<br>
            </div>
            <blockquote cite="mid:D1B1D466.6B82%25ah259@hw.ac.uk"
              type="cite">
              <div>
                <div>Dear All,</div>
                <div><br>
                </div>
                <div>I am simulating carbon nanotubes in solvent,
                  approximating the tubes as rigid cylinders using the
                  freeze group function to hold the CNT atoms in place.</div>
                <div><br>
                </div>
                <div>To do this correctly I need to modify the virial. I
                  have already excluded the solid (frozen) groups from
                  the virial calculation but now what I require is to
                  exclude the shifted part of the virial calculation
                  (second part of equation B.11 in the gromacs manual)
                  for only the solid/fluid interactions.†</div>
                <div><br>
                </div>
                <div>My initial assessment is that it may be easier to
                  calculate this contribution after the fact and
                  subtract this from the total virial. The difficulty I
                  find is that in the part of the code where the virial
                  is calculated the forces have already been summed up
                  on each atom and I donít see any way to access the
                  pairwise forces which I believe are necessary to do
                  what I want. Iíve looked at non-bonded force
                  calculations in the source code and it frankly scares
                  the hell out of me so I wouldnít even know where to
                  start.</div>
                <div><br>
                </div>
                <div>I am assuming there are no functions within the
                  code already that might allow me to do this.</div>
                <div><br>
                </div>
                <div>Can anyone give me any suggestions? I guess ideally
                  I would be looking to find some sort of data structure
                  which contains all the pair-wise forces at some point
                  and I can work from there. Does this exist?</div>
                <div><br>
                </div>
                <div><br>
                </div>
                <div>Many thanks,</div>
                <div><br>
                </div>
                <div><br>
                </div>
                <div>Adam</div>
                <div><br>
                </div>
              </div>
              <div>
                <div>----------------------------------------------------------</div>
                <div>Adam Hardy</div>
                <div>PhD Student</div>
                <div>School of Engineering and Physical Sciences</div>
                <div>Heriot Watt University</div>
                <div>Edinburgh, EH14 4AS</div>
                <div>Phone: +441314513074</div>
                <div><a moz-do-not-send="true"
                    class="moz-txt-link-abbreviated"
                    href="mailto:ah259@hw.ac.uk">ah259@hw.ac.uk</a></div>
                <div>----------------------------------------------------------</div>
              </div>
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