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    On 11/02/2012 4:15 AM, francesca vitalini wrote:
    <blockquote
cite="mid:CAPRCF+KByUCD91m_yo_+X3MWf0=t8PWOktfd7zuGYY5qo5xn5A@mail.gmail.com"
      type="cite">Ok now I have tryied to restart it all and the problem
      seems to be that the system has some overlapping. In fact, no
      matter what I freeze, water, CA or nothing, I get this error
      message<br>
      <br>
      &nbsp;VERSION 3.3.1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>
      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;
      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>
      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; This program is free software; you can redistribute it
      and/or<br>
      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; modify it under the terms of the GNU General Public
      License<br>
      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; as published by the Free Software Foundation; either
      version 2<br>
      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; of the License, or (at your option) any later
      version.<br>
      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; If you want to redistribute modifications, please consider
      that<br>
      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; scientific software is very special. Version control is
      crucial-<br>
      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; bugs must be traceable. We will be happy to consider code
      for<br>
      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; inclusion in the official distribution, but derived work
      must not<br>
      &nbsp;&nbsp;&nbsp;&nbsp; be called official GROMACS. Details are found in the README
      &amp; COPYING<br>
      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; files.<br>
      <br>
      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; :-)&nbsp; gaia30&nbsp; (-:<br>
      <br>
      Option&nbsp;&nbsp;&nbsp;&nbsp; Filename&nbsp; Type&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Description<br>
      ------------------------------------------------------------<br>
      &nbsp; -s&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; EM3.tpr&nbsp; Input&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Generic run input: tpr tpb tpa
      xml<br>
      &nbsp; -o&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; EM3.trr&nbsp; Output&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Full precision trajectory: trr
      trj<br>
      &nbsp; -x&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; EM3.xtc&nbsp; Output, Opt! Compressed trajectory (portable
      xdr format)<br>
      &nbsp; -c&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; EM3.gro&nbsp; Output&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Generic structure: gro g96 pdb
      xml<br>
      &nbsp; -e&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; EM3.edr&nbsp; Output&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Generic energy: edr ene<br>
      &nbsp; -g&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; EM3.log&nbsp; Output&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Log file<br>
      -dgdl&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; EM3.xvg&nbsp; Output, Opt. xvgr/xmgr file<br>
      -field&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; EM3.xvg&nbsp; Output, Opt. xvgr/xmgr file<br>
      -table&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; EM3.xvg&nbsp; Input, Opt.&nbsp; xvgr/xmgr file<br>
      -tablep&nbsp;&nbsp;&nbsp;&nbsp; EM3.xvg&nbsp; Input, Opt.&nbsp; xvgr/xmgr file<br>
      -rerun&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; EM3.trr&nbsp; Input, Opt.&nbsp; Generic trajectory: xtc trr trj
      gro g96 pdb<br>
      -tpi&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; EM3.xvg&nbsp; Output, Opt. xvgr/xmgr file<br>
      &nbsp;-ei&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; EM3.edi&nbsp; Input, Opt.&nbsp; ED sampling input<br>
      &nbsp;-eo&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; EM3.edo&nbsp; Output, Opt. ED sampling output<br>
      &nbsp; -j&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; EM3.gct&nbsp; Input, Opt.&nbsp; General coupling stuff<br>
      &nbsp;-jo&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; EM3.gct&nbsp; Output, Opt. General coupling stuff<br>
      -ffout&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; EM3.xvg&nbsp; Output, Opt. xvgr/xmgr file<br>
      -devout&nbsp;&nbsp;&nbsp;&nbsp; EM3.xvg&nbsp; Output, Opt. xvgr/xmgr file<br>
      -runav&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; EM3.xvg&nbsp; Output, Opt. xvgr/xmgr file<br>
      &nbsp;-pi&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; EM3.ppa&nbsp; Input, Opt.&nbsp; Pull parameters<br>
      &nbsp;-po&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; EM3.ppa&nbsp; Output, Opt. Pull parameters<br>
      &nbsp;-pd&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; EM3.pdo&nbsp; Output, Opt. Pull data output<br>
      &nbsp;-pn&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; EM3.ndx&nbsp; Input, Opt.&nbsp; Index file<br>
      -mtx&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; EM3.mtx&nbsp; Output, Opt. Hessian matrix<br>
      &nbsp;-dn&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; EM3.ndx&nbsp; Output, Opt. Index file<br>
      -coarse&nbsp;&nbsp;&nbsp;&nbsp; ION.gro&nbsp; Input&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Generic trajectory: xtc trr trj
      gro g96 pdb<br>
      <br>
      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Option&nbsp;&nbsp; Type&nbsp; Value&nbsp; Description<br>
      ------------------------------------------------------<br>
      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -[no]h&nbsp;&nbsp; bool&nbsp;&nbsp;&nbsp;&nbsp; no&nbsp; Print help info and quit<br>
      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -nice&nbsp;&nbsp;&nbsp; int&nbsp;&nbsp;&nbsp;&nbsp; 19&nbsp; Set the nicelevel<br>
      &nbsp;&nbsp;&nbsp;&nbsp; -deffnm string&nbsp;&nbsp;&nbsp; EM3&nbsp; Set the default filename for all file
      options<br>
      &nbsp;&nbsp; -[no]xvgr&nbsp;&nbsp; bool&nbsp;&nbsp;&nbsp; yes&nbsp; Add specific codes (legends etc.) in
      the output<br>
      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; xvg files for the xmgrace program<br>
      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -np&nbsp;&nbsp;&nbsp; int&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp; Number of nodes, must be the same as
      used for<br>
      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; grompp<br>
      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -nt&nbsp;&nbsp;&nbsp; int&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp; Number of threads to start on each
      node<br>
      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -[no]v&nbsp;&nbsp; bool&nbsp;&nbsp;&nbsp; yes&nbsp; Be loud and noisy<br>
      -[no]compact&nbsp;&nbsp; bool&nbsp;&nbsp;&nbsp; yes&nbsp; Write a compact log file<br>
      -[no]sepdvdl&nbsp;&nbsp; bool&nbsp;&nbsp;&nbsp;&nbsp; no&nbsp; Write separate V and dVdl terms for
      each<br>
      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; interaction type and node to the log
      file(s)<br>
      &nbsp; -[no]multi&nbsp;&nbsp; bool&nbsp;&nbsp;&nbsp;&nbsp; no&nbsp; Do multiple simulations in parallel
      (only with<br>
      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -np &gt; 1)<br>
      &nbsp;&nbsp;&nbsp;&nbsp; -replex&nbsp;&nbsp;&nbsp; int&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp; Attempt replica exchange every # steps<br>
      &nbsp;&nbsp;&nbsp;&nbsp; -reseed&nbsp;&nbsp;&nbsp; int&nbsp;&nbsp;&nbsp;&nbsp; -1&nbsp; Seed for replica exchange, -1 is
      generate a seed<br>
      &nbsp;&nbsp; -[no]glas&nbsp;&nbsp; bool&nbsp;&nbsp;&nbsp;&nbsp; no&nbsp; Do glass simulation with special long
      range<br>
      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; corrections<br>
      &nbsp;-[no]ionize&nbsp;&nbsp; bool&nbsp;&nbsp;&nbsp;&nbsp; no&nbsp; Do a simulation including the effect
      of an X-Ray<br>
      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; bombardment on your system<br>
      <br>
      <br>
      Back Off! I just backed up EM3.log to ./#EM3.log.2#<br>
      Getting Loaded...<br>
      Reading file EM3.tpr, VERSION 3.3.1 (single precision)<br>
      Loaded with Money<br>
      <br>
      <br>
      Back Off! I just backed up EM3.edr to ./#EM3.edr.2#<br>
      Steepest Descents:<br>
      &nbsp;&nbsp; Tolerance (Fmax)&nbsp;&nbsp; =&nbsp; 1.00000e+01<br>
      &nbsp;&nbsp; Number of steps&nbsp;&nbsp;&nbsp; =&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 200<br>
      -------------------------------------------------------&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
      inf, atom= 15321<br>
      Program mdrun, VERSION 3.3.1<br>
      Source code file: nsgrid.c, line: 226<br>
      <br>
      Range checking error:<br>
      Explanation: During neighborsearching, we assign each particle to
      a grid<br>
      based on its coordinates. If your system contains collisions or
      parameter<br>
      errors that give particles very high velocities you might end up
      with some<br>
      coordinates being +-Infinity or NaN (not-a-number). Obviously, we
      cannot<br>
      put these on a grid, so this is usually where we detect those
      errors.<br>
      Make sure your system is properly energy-minimized and that the
      potential<br>
      energy seems reasonable before trying again.<br>
      <br>
      Variable ci has value -2147483648. It should have been within [ 0
      .. 42875 ]<br>
      Please report this to the mailing list (<a moz-do-not-send="true"
        href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>)<br>
      -------------------------------------------------------<br>
      <br>
      "With a Lead Filled Snowshoe" (F. Zappa)<br>
      <br>
      Halting program mdrun<br>
      <br>
      gcq#159: "With a Lead Filled Snowshoe" (F. Zappa)<br>
      <br>
--------------------------------------------------------------------------<br>
      MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD <br>
      with errorcode -1.<br>
      <br>
      NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI
      processes.<br>
      You may or may not see output from other processes, depending on<br>
      exactly when Open MPI kills them.<br>
      <br>
      <br>
      So... How ca I overcome the issue of overlapping atoms?<br>
    </blockquote>
    <br>
    Generate better FG structures using a better method.<br>
    <br>
    Try vacuum MD or SA with tiny time steps and no bond constraints.<br>
    <br>
    Mark<br>
    <br>
    <blockquote
cite="mid:CAPRCF+KByUCD91m_yo_+X3MWf0=t8PWOktfd7zuGYY5qo5xn5A@mail.gmail.com"
      type="cite">Thanks<br>
      Fra<br>
      <br>
      <div class="gmail_quote">2012/2/10 francesca vitalini <span
          dir="ltr">&lt;<a moz-do-not-send="true"
            href="mailto:francesca.vitalini11@gmail.com">francesca.vitalini11@gmail.com</a>&gt;</span><br>
        <blockquote class="gmail_quote" style="margin:0 0 0
          .8ex;border-left:1px #ccc solid;padding-left:1ex">In fact in
          the reverse transformation I'm feeding the CG structure
          information. <br>
          Once I look through VMD to the FG structure I notice that the
          backbones are not in planes so definitely I need to run some
          minimization there. In the tutorial they were using simulating
          annealing, but I don't think I need more than energy
          minimization for that.<br>
          What do you think?
          <div class="HOEnZb">
            <div class="h5"><br>
              <br>
              <br>
              <br>
              <div class="gmail_quote">2012/2/10 Mark Abraham <span
                  dir="ltr">&lt;<a moz-do-not-send="true"
                    href="mailto:Mark.Abraham@anu.edu.au"
                    target="_blank">Mark.Abraham@anu.edu.au</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>
                      <div> On 11/02/2012 12:41 AM, francesca vitalini
                        wrote:
                        <blockquote type="cite">In order to overcome the
                          problem I tried to fix everything except the
                          backbone (solvent, sidechain and CA, as I want
                          the structure to be maintained). However, if I
                          do then I have problems with the energy
                          minimization as the force on the 15300 is
                          infinite.<br>
                          <br>
                          Getting Loaded...<br>
                          Reading file EM1-1.tpr, VERSION 3.3.1 (single
                          precision)<br>
                          Loaded with Money<br>
                          <br>
                          Steepest Descents:<br>
                          &nbsp;&nbsp; Tolerance (Fmax)&nbsp;&nbsp; =&nbsp; 1.00000e+01<br>
                          &nbsp;&nbsp; Number of steps&nbsp;&nbsp;&nbsp; =&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2000<br>
                          -------------------------------------------------------&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;

                          inf, atom= 15300<br>
                          Program mdrun, VERSION 3.3.1<br>
                          Source code file: nsgrid.c, line: 226<br>
                          <br>
                          Range checking error:<br>
                          Explanation: During neighborsearching, we
                          assign each particle to a grid<br>
                          based on its coordinates. If your system
                          contains collisions or parameter<br>
                          errors that give particles very high
                          velocities you might end up with some<br>
                          coordinates being +-Infinity or NaN
                          (not-a-number). Obviously, we cannot<br>
                          put these on a grid, so this is usually where
                          we detect those errors.<br>
                          Make sure your system is properly
                          energy-minimized and that the potential<br>
                          energy seems reasonable before trying again.<br>
                          <br>
                          Variable ci has value -<a
                            moz-do-not-send="true" href="tel:2147483648"
                            value="+12147483648" target="_blank">2147483648</a>.
                          It should have been within [ 0 .. 27744 ]<br>
                          Please report this to the mailing list (<a
                            moz-do-not-send="true"
                            href="mailto:gmx-users@gromacs.org"
                            target="_blank">gmx-users@gromacs.org</a>)<br>
-------------------------------------------------------<br>
                          <br>
                          "Oh My God ! It's the Funky Shit" (Beastie
                          Boys)<br>
                          <br>
                          Halting program mdrun<br>
                          <br>
                          You suggested to check if there is any
                          overlapping.</blockquote>
                        <br>
                      </div>
                    </div>
                    ... so you need to get out some visualization
                    software and look at the transformed structure :)
                    <div><br>
                      <br>
                      <blockquote type="cite"> There might be as my
                        structure is obtained through a reverse
                        transformation from a CG representation. In the
                        mapping the atoms are positioned randomly in the
                        bead. Now I'm running some energy minimization
                        to equilibrate those atoms. I had to solvate the
                        system after the mapping (couldn't do it before
                        due to problems with ions)but I haven't
                        equilibrated it yet and I'm keeping it fixed
                        which could also be a source of overlapping. <br>
                      </blockquote>
                      <br>
                    </div>
                    Local minimization with EM cannot in general take a
                    "random" positioning of the generated atoms and make
                    it one that will be stable under MD. Some structure
                    knowledge needs to be build into the reverse
                    transformation.<span><font color="#888888"><br>
                        <br>
                        Mark</font></span>
                    <div>
                      <div><br>
                        <br>
                        <blockquote type="cite"> Any ideas?<br>
                          Thanks.<br>
                          Francesca<br>
                          <br>
                          <br>
                          <div class="gmail_quote">2012/2/10 Justin A.
                            Lemkul <span dir="ltr">&lt;<a
                                moz-do-not-send="true"
                                href="mailto:jalemkul@vt.edu"
                                target="_blank">jalemkul@vt.edu</a>&gt;</span><br>
                            <blockquote class="gmail_quote"
                              style="margin:0 0 0 .8ex;border-left:1px
                              #ccc solid;padding-left:1ex">
                              <div><br>
                                <br>
                                francesca vitalini wrote:<br>
                                <blockquote class="gmail_quote"
                                  style="margin:0 0 0
                                  .8ex;border-left:1px #ccc
                                  solid;padding-left:1ex"> I achieve<br>
                                  <br>
                                  Steepest Descents converged to machine
                                  precision in 205 steps,<br>
                                  but did not reach the requested Fmax
                                  &lt; 10.<br>
                                  Potential Energy &nbsp;=
                                  -1.49131940478719e+07<br>
                                  Maximum force &nbsp; &nbsp; =
                                  &nbsp;1.09664530279637e+06 on atom 1520 &nbsp;
                                  &nbsp;(parto of the protein)<br>
                                  Norm of force &nbsp; &nbsp; =
                                  &nbsp;2.28369808518165e+06<br>
                                  <br>
                                </blockquote>
                                <br>
                              </div>
                              The magnitude of the force suggests atomic
                              overlap somewhere. &nbsp;Start by investigating
                              the environment around atom 1520.
                              <div><br>
                                <br>
                                <blockquote class="gmail_quote"
                                  style="margin:0 0 0
                                  .8ex;border-left:1px #ccc
                                  solid;padding-left:1ex"> and the
                                  system looked with vmd doesn't look as
                                  if it was exploding. However, I have
                                  warnings about the table extension and
                                  I don't know why but gromacs writes
                                  pdb files sometime. However I thought
                                  that there <br>
                                </blockquote>
                                <br>
                              </div>
                              The "step.pdb" files are written when
                              mdrun is about to crash.
                              <div><br>
                                <br>
                                <blockquote class="gmail_quote"
                                  style="margin:0 0 0
                                  .8ex;border-left:1px #ccc
                                  solid;padding-left:1ex"> might have
                                  been an error in the way I defined the
                                  position restraints, in fact in the
                                  mdp file I hade define = -DEPOSRE
                                  while in the topology I had ifdef
                                  DEFINE_WAT, so it might have moved it
                                  all without fixing the water. So I
                                  tried again and this time I got<br>
                                  <br>
                                </blockquote>
                                <br>
                              </div>
                              The "define" statements are literal, so be
                              careful of typos. &nbsp;-DEPOSRE will not work
                              when the topology calls for -DPOSRES. &nbsp;So
                              unless you've changed default naming for
                              "define" statements, you're not going to
                              get what you expect.
                              <div> <br>
                                <br>
                                <blockquote class="gmail_quote"
                                  style="margin:0 0 0
                                  .8ex;border-left:1px #ccc
                                  solid;padding-left:1ex"> Steepest
                                  Descents converged to machine
                                  precision in 72 steps,<br>
                                  but did not reach the requested Fmax
                                  &lt; 10.<br>
                                  Potential Energy &nbsp;= -2.0135496e+07<br>
                                  Maximum force &nbsp; &nbsp; = &nbsp;2.0486184e+12 on
                                  atom 4479<br>
                                  Norm of force &nbsp; &nbsp; = &nbsp;7.2424045e+13<br>
                                  <br>
                                </blockquote>
                                <br>
                              </div>
                              Again, symptomatic of severe atomic
                              overlap.
                              <div><br>
                                <br>
                                <blockquote class="gmail_quote"
                                  style="margin:0 0 0
                                  .8ex;border-left:1px #ccc
                                  solid;padding-left:1ex"> but again the
                                  same issue with table extent and still
                                  the production of pdb files.<br>
                                  <br>
                                  Any explanations?<br>
                                  <br>
                                </blockquote>
                                <br>
                              </div>
                              Investigate the starting configurations
                              near the problematic atoms.<br>
                              <br>
                              <a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System"
                                target="_blank">http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System</a><span><font
                                  color="#888888"><br>
                                  <br>
                                  -Justin</font></span>
                              <div>
                                <div><br>
                                  <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]<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"
                                    value="+15402319080" target="_blank">(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>
========================================<br>
                                  -- <br>
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                                </div>
                              </div>
                            </blockquote>
                          </div>
                          <br>
                          <br clear="all">
                          <br>
                          -- <br>
                          Francesca Vitalini<br>
                          <br>
                          PhD student at Computational Molecular Biology
                          Group, <br>
                          Department of Mathematics and Informatics,
                          FU-Berlin<br>
                          Arnimallee 6 14195 Berlin<br>
                          <br>
                          <a moz-do-not-send="true"
                            href="mailto:vitalini@zedat.fu-berlin.de"
                            target="_blank">vitalini@zedat.fu-berlin.de</a><br>
                          <a moz-do-not-send="true"
                            href="mailto:francesca.vitalini@fu-berlin.de"
                            target="_blank">francesca.vitalini@fu-berlin.de</a><br>
                          <br>
                          <a moz-do-not-send="true"
                            href="tel:%2B49%203083875776"
                            value="+493083875776" target="_blank">+49
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                          <br>
                          <br>
                          <fieldset></fieldset>
                          <br>
                        </blockquote>
                        <br>
                      </div>
                    </div>
                  </div>
                  <br>
                  --<br>
                  gmx-users mailing list &nbsp; &nbsp;<a moz-do-not-send="true"
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                </blockquote>
              </div>
              <br>
              <br clear="all">
              <br>
              -- <br>
              Francesca Vitalini<br>
              <br>
              PhD student at Computational Molecular Biology Group, <br>
              Department of Mathematics and Informatics, FU-Berlin<br>
              Arnimallee 6 14195 Berlin<br>
              <br>
              <a moz-do-not-send="true"
                href="mailto:vitalini@zedat.fu-berlin.de"
                target="_blank">vitalini@zedat.fu-berlin.de</a><br>
              <a moz-do-not-send="true"
                href="mailto:francesca.vitalini@fu-berlin.de"
                target="_blank">francesca.vitalini@fu-berlin.de</a><br>
              <br>
              <a moz-do-not-send="true" href="tel:%2B49%203083875776"
                value="+493083875776" target="_blank">+49 3083875776</a><br>
              <a moz-do-not-send="true" href="tel:%2B49%203083875412"
                value="+493083875412" target="_blank">+49 3083875412</a><br>
              <br>
            </div>
          </div>
        </blockquote>
      </div>
      <br>
      <br clear="all">
      <br>
      -- <br>
      Francesca Vitalini<br>
      <br>
      PhD student at Computational Molecular Biology Group, <br>
      Department of Mathematics and Informatics, FU-Berlin<br>
      Arnimallee 6 14195 Berlin<br>
      <br>
      <a moz-do-not-send="true"
        href="mailto:vitalini@zedat.fu-berlin.de" target="_blank">vitalini@zedat.fu-berlin.de</a><br>
      <a moz-do-not-send="true"
        href="mailto:francesca.vitalini@fu-berlin.de" target="_blank">francesca.vitalini@fu-berlin.de</a><br>
      <br>
      +49 3083875776<br>
      +49 3083875412<br>
      <br>
      <br>
      <fieldset class="mimeAttachmentHeader"></fieldset>
      <br>
    </blockquote>
    <br>
  </body>
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