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    On 16/11/2011 2:45 PM, Liu, Liang wrote:
    <blockquote
cite="mid:CABxJRoKMoQBPhuGMY_km7diBD-u4EPoiQGo0kNZKCjUn6nVmpA@mail.gmail.com"
      type="cite"><font color="#000099"><font face="verdana,sans-serif">Thanks
          for help.</font></font>
      <div><font color="#000099"><font face="verdana,sans-serif">If I
            have more atoms and they can interact each other or itself,
            like PP, PC, PN, CP, CN, CC .... How's the energygrp_table
            looking like?</font></font></div>
      <div><font class="Apple-style-span" color="#000099" face="verdana,
          sans-serif">I know there should be a option in the grompp, but
          how to do that?</font></div>
    </blockquote>
    <br>
    See manual sections 7.3.12 and 6.7.2.<br>
    <br>
    <blockquote
cite="mid:CABxJRoKMoQBPhuGMY_km7diBD-u4EPoiQGo0kNZKCjUn6nVmpA@mail.gmail.com"
      type="cite">
      <div><font class="Apple-style-span" color="#000099" face="verdana,
          sans-serif"> And how to generate the index file? I am sorry
          for so many questions, I am really not familiar with it.</font></div>
    </blockquote>
    <br>
    <a
      href="http://www.gromacs.org/Documentation/File_Formats/Index_File">http://www.gromacs.org/Documentation/File_Formats/Index_File</a><br>
    <br>
    Mark<br>
    <br>
    <blockquote
cite="mid:CABxJRoKMoQBPhuGMY_km7diBD-u4EPoiQGo0kNZKCjUn6nVmpA@mail.gmail.com"
      type="cite">
      <div><br>
        <div class="gmail_quote">On Tue, Nov 15, 2011 at 9:28 PM,
          Sikandar Mashayak <span dir="ltr">&lt;<a
              moz-do-not-send="true" href="mailto:symashayak@gmail.com">symashayak@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;">
            &gt;From your system information, I understand that you need
            to specify tabulated potentials between atoms P and P, and
            between atoms C and P, and so on. <br>
            <br>
            To achieve this, you need to create energy groups with atom
            types P and C, and specify energygrp_table options in the
            grompp such as following<br>
            <br>
            ....<br>
            <br>
            energygrps = P C ; (and rest of the groups in your system,
            you will need to specify index file containing energy groups
            ) <br>
            energygrp_table = P P P C<br>
            <br>
            ....<br>
            <br>
            so now mdrun looks for table_P_P.xvg and table_P_C.xvg in
            the run directory, and uses it for P-P and P-C interactions,
            whereas for all other interactions default table.xvg file is
            used.<br>
            <br>
            <br>
            I hope this helps.<br>
            <br>
            Regards<br>
            Sikandar<br>
            <br>
            <br>
            <div class="gmail_quote">
              <div>
                <div class="h5">On Tue, Nov 15, 2011 at 2:49 PM, Liu,
                  Liang <span dir="ltr">&lt;<a moz-do-not-send="true"
                      href="mailto:liu4gre@gmail.com" target="_blank">liu4gre@gmail.com</a>&gt;</span>
                  wrote:<br>
                </div>
              </div>
              <blockquote class="gmail_quote" style="margin:0 0 0
                .8ex;border-left:1px #ccc solid;padding-left:1ex">
                <div>
                  <div class="h5"><font color="#000099"><font
                        face="verdana,sans-serif">I am trying to use a
                        serial of tabulated potentials, which are the
                        functions of the distance between atoms and the
                        names are table.xvg, table_P_P.xvg,
                        table_C_P.xvg, etc., to do the energy
                        minimization of some RNA structures.</font></font>
                    <div>
                      <font color="#000099"><font
                          face="verdana,sans-serif">The procedure I
                          apply is as following:</font></font></div>
                    <div><font color="#000099"><font
                          face="verdana,sans-serif"><br>
                        </font></font></div>
                    <div><font color="#000099"><font
                          face="verdana,sans-serif">
                          <div>
                            pdb2gmx -f rna.pdb -o conf.pdb -ff amber03
                            -water spce</div>
                          <div>editconf -bt octahedron -f conf.pdb -o
                            box.pdb -d 1.0</div>
                          <div>genbox -cp box.pdb -cs spc216 -o
                            water.pdb -p topol.top</div>
                          <div>grompp -f em.mdp -c water.pdb -p
                            topol.top -o em.tpr -maxwarn 2</div>
                          <div>mdrun -v -s em.tpr -c em.pdb -table
                            table.xvg</div>
                          <div><br>
                          </div>
                          <div>And the em.mdp file is:</div>
                          <div>
                            <div>cpp &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;/usr/bin/cpp &nbsp; &nbsp;
                              &nbsp; &nbsp; &nbsp; &nbsp;; Preprocessor</div>
                            <div>include &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;-I../top &nbsp; &nbsp; &nbsp; &nbsp;
                              &nbsp; &nbsp; &nbsp; &nbsp;; Directories to include in the
                              topology format</div>
                            <div>define &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;-DFLEX_SPC</div>
                            <div>integrator &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;steep &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
                              &nbsp; &nbsp; &nbsp; &nbsp; ; Algorithm options</div>
                            <div>dt &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;0.002 &nbsp; &nbsp;; ps !
                              &nbsp; &nbsp; &nbsp; &nbsp; ; run control, the time step</div>
                            <div>nsteps &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;1000 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
                              &nbsp; &nbsp; &nbsp; &nbsp;; run steps, simulation length =
                              dt*nsteps</div>
                            <div>nstenergy &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;10 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
                              &nbsp; &nbsp; &nbsp; &nbsp;; Write energies to disk every
                              nstenergy steps</div>
                            <div>nstxtcout &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;10 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
                              &nbsp; &nbsp; &nbsp; &nbsp;; Write coordinates to disk every
                              nstxtcout steps</div>
                            <div>xtc_grps &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;RNA &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
                              &nbsp; &nbsp; &nbsp; &nbsp; ; Which coordinate group(s) to
                              write to disk</div>
                            <div>energygrps &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;RNA &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
                              &nbsp; &nbsp; &nbsp; &nbsp; ; Whici energy group(s) to write
                              to disk</div>
                            <div>nstlist &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;10 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
                              &nbsp; &nbsp; &nbsp; &nbsp;; Frequency to update the neighbor
                              list and long range forces</div>
                            <div>
                              ns_type &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;grid &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
                              &nbsp; &nbsp; &nbsp;; Method to determine neighbor list
                              and long range forces (simple, grid)</div>
                            <div>rlist &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;1.0 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
                              &nbsp; &nbsp; &nbsp; &nbsp; ; Cut-off for making neighbor list
                              (short range forces)</div>
                            <div>vdw-type &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;user</div>
                            <div>coulombtype &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;user &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
                              &nbsp; &nbsp; &nbsp; &nbsp;; Treatment of long range
                              electrostatic interactions</div>
                            <div>rcoulomb &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;1.0 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
                              &nbsp; &nbsp; &nbsp; &nbsp; ; long range electrostatic cut-off</div>
                            <div>rvdw &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;1.0 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
                              &nbsp; &nbsp; &nbsp; &nbsp; ; long range Van der Walls cut-off</div>
                            <div>constraints &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;none</div>
                            <div>pbc &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;xyz</div>
                            <div>emtol &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;5000.0</div>
                            <div>emstep &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;0.01</div>
                          </div>
                        </font></font>
                      <div><br>
                      </div>
                      <div>All the procedure and file are right? Thanks.</div>
                      <span><font color="#888888">
                          <div><br>
                          </div>
                          -- <br>
                          Best,<br>
                          Liang Liu<br>
                        </font></span></div>
                    <br>
                  </div>
                </div>
                <span class="HOEnZb"><font color="#888888">--<br>
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                  </font></span></blockquote>
            </div>
            <br>
            <br>
            --<br>
            gmx-users mailing list &nbsp; &nbsp;<a moz-do-not-send="true"
              href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
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            Please don't post (un)subscribe requests to the list. Use
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          </blockquote>
        </div>
        <br>
        <br clear="all">
        <div><br>
        </div>
        -- <br>
        Best,<br>
        Liang Liu<br>
      </div>
      <br>
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      <br>
    </blockquote>
    <br>
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