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<div class=Section1>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Does anybody understand this <span class=GramE>behavior:</span><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><span class=GramE><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>node1-claudiom</span></font></span><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'> 63 % <span
class=SpellE>pwd</span><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>/scratch/claudiom/111<o:p></o:p></span></font></p>
<p class=MsoNormal><span class=GramE><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>node1-claudiom</span></font></span><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'> 64 % <span
class=SpellE>ls</span><o:p></o:p></span></font></p>
<p class=MsoNormal><span class=SpellE><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>topol.tpr</span></font></span><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'><o:p></o:p></span></font></p>
<p class=MsoNormal><span class=GramE><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>node1-claudiom</span></font></span><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'> 65 % <span
class=SpellE>mdrun</span><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><span
style='mso-spacerun:yes'>
</span>:-)<span style='mso-spacerun:yes'> </span>G<span
style='mso-spacerun:yes'> </span><span class=GramE>R<span
style='mso-spacerun:yes'> </span>O</span><span
style='mso-spacerun:yes'> </span>M<span style='mso-spacerun:yes'>
</span>A<span style='mso-spacerun:yes'> </span>C<span
style='mso-spacerun:yes'> </span>S<span style='mso-spacerun:yes'>
</span>(-:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><span
style='mso-spacerun:yes'>
</span><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Segmentation fault<o:p></o:p></span></font></p>
<p class=MsoNormal><span class=GramE><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>node1-claudiom</span></font></span><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'> 66 %<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>BUT CHECK THIS OUT<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><span class=GramE><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>node1-claudiom</span></font></span><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'> 66 % <span
class=SpellE>pwd</span><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>/scratch/claudiom/111<o:p></o:p></span></font></p>
<p class=MsoNormal><span class=GramE><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>node1-claudiom</span></font></span><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'> 67 % <span
class=SpellE>cd</span> ..<o:p></o:p></span></font></p>
<p class=MsoNormal><span class=GramE><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>node1-claudiom</span></font></span><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'> 68 % <span
class=SpellE>pwd</span><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>/scratch/<span class=SpellE>claudiom</span><o:p></o:p></span></font></p>
<p class=MsoNormal><span class=GramE><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>node1-claudiom</span></font></span><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'> 69 % <span
class=SpellE>mv</span> 111 <span class=SpellE>tt</span><o:p></o:p></span></font></p>
<p class=MsoNormal><span class=GramE><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>node1-claudiom</span></font></span><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'> 70 % <span
class=SpellE>cd</span> <span class=SpellE>tt</span><o:p></o:p></span></font></p>
<p class=MsoNormal><span class=GramE><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>node1-claudiom</span></font></span><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'> 71 % <span
class=SpellE>pwd</span><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>/scratch/<span class=SpellE>claudiom/tt</span><o:p></o:p></span></font></p>
<p class=MsoNormal><span class=GramE><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>node1-claudiom</span></font></span><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'> 72 % <span
class=SpellE>mdrun</span><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><span
style='mso-spacerun:yes'>
</span>:-)<span style='mso-spacerun:yes'> </span>G<span
style='mso-spacerun:yes'> </span><span class=GramE>R<span
style='mso-spacerun:yes'> </span>O</span><span
style='mso-spacerun:yes'> </span>M<span style='mso-spacerun:yes'>
</span>A<span style='mso-spacerun:yes'> </span>C<span
style='mso-spacerun:yes'> </span>S<span style='mso-spacerun:yes'>
</span>(-:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><span
style='mso-spacerun:yes'>
</span><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><span
style='mso-spacerun:yes'>
</span>Green Red </span></font><st1:place><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>Orange</span></font></st1:place><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'> Magenta
Azure Cyan <span class=SpellE>Skyblue</span><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><span
style='mso-spacerun:yes'>
</span><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><span
style='mso-spacerun:yes'>
</span>:-)<span style='mso-spacerun:yes'> </span>VERSION <span
class=GramE>3.1.4<span style='mso-spacerun:yes'> </span>(</span>-:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><span
style='mso-spacerun:yes'>
</span><span
style='mso-spacerun:yes'> </span><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><span
style='mso-spacerun:yes'>
</span><span
style='mso-spacerun:yes'> </span><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><span
style='mso-spacerun:yes'> </span>Copyright
(c) 1991-2002, </span></font><st1:place><st1:PlaceType><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>University</span></font></st1:PlaceType><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'> of </span></font><st1:PlaceName><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'>Groningen</span></font></st1:PlaceName></st1:place><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'>, <span
class=GramE>The</span> </span></font><st1:country-region><st1:place><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'>Netherlands</span></font></st1:place></st1:country-region><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><span
style='mso-spacerun:yes'>
</span>This program is free software; you can redistribute it and/or<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><span
style='mso-spacerun:yes'>
</span><span class=GramE>modify</span> it under the terms of the GNU General
Public License<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><span
style='mso-spacerun:yes'>
</span><span class=GramE>as</span> published by the Free Software Foundation;
either version 2<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><span
style='mso-spacerun:yes'>
</span><span class=GramE>of</span> the License, or (at your option) any later
version.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><span
style='mso-spacerun:yes'>
</span><span
style='mso-spacerun:yes'> </span><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><span
style='mso-spacerun:yes'>
</span>:-<span class=GramE>)<span style='mso-spacerun:yes'> </span><span
class=SpellE>mdrun</span></span><span style='mso-spacerun:yes'>
</span>(-:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><span
style='mso-spacerun:yes'>
</span><span
style='mso-spacerun:yes'> </span><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Option<span
style='mso-spacerun:yes'> </span><span class=GramE>Filename<span
style='mso-spacerun:yes'> </span>Type</span><span
style='mso-spacerun:yes'>
</span>Description<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>------------------------------------------------------------<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><span style='mso-spacerun:yes'> </span>-s<span
style='mso-spacerun:yes'> </span><span
class=SpellE><span class=GramE>topol.tpr</span></span><span class=GramE><span
style='mso-spacerun:yes'> </span>Input</span><span
style='mso-spacerun:yes'>
</span>Generic run input: <span class=SpellE>tpr</span> <span class=SpellE>tpb</span>
<span class=SpellE>tpa</span><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><span style='mso-spacerun:yes'> </span>-o<span
style='mso-spacerun:yes'> </span><span
class=SpellE><span class=GramE>traj.trr</span></span><span class=GramE><span
style='mso-spacerun:yes'> </span>Output</span><span
style='mso-spacerun:yes'> </span>Full
precision trajectory: <span class=SpellE>trr</span> <span class=SpellE>trj</span><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><span style='mso-spacerun:yes'> </span>-x<span
style='mso-spacerun:yes'> </span><span
class=SpellE><span class=GramE>traj.xtc</span></span><span class=GramE><span
style='mso-spacerun:yes'> </span>Output</span>, Opt.<span
style='mso-spacerun:yes'> </span>Compressed trajectory (portable <span
class=SpellE>xdr</span> format)<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><span style='mso-spacerun:yes'> </span>-c<span
style='mso-spacerun:yes'> </span><span class=SpellE><span
class=GramE>confout.gro</span></span><span class=GramE><span
style='mso-spacerun:yes'> </span>Output</span><span
style='mso-spacerun:yes'>
</span>Generic structure: <span class=SpellE>gro</span> g96 <span class=SpellE>pdb</span><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><span style='mso-spacerun:yes'> </span>-e<span
style='mso-spacerun:yes'> </span><span
class=SpellE><span class=GramE>ener.edr</span></span><span class=GramE><span
style='mso-spacerun:yes'> </span>Output</span><span
style='mso-spacerun:yes'>
</span>Generic energy: <span class=SpellE>edr</span> <span class=SpellE>ene</span><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><span style='mso-spacerun:yes'> </span>-g<span
style='mso-spacerun:yes'>
</span><span class=SpellE><span class=GramE>md.log</span></span><span
class=GramE><span style='mso-spacerun:yes'> </span>Output</span><span
style='mso-spacerun:yes'> </span>Log
file<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>-<span class=SpellE>dgdl</span><span
style='mso-spacerun:yes'> </span><span
class=SpellE><span class=GramE>dgdl.xvg</span></span><span class=GramE><span
style='mso-spacerun:yes'> </span>Output</span>, Opt.<span
style='mso-spacerun:yes'> </span><span class=SpellE><span class=GramE>xvgr/xmgr</span></span>
file<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>-table<span style='mso-spacerun:yes'>
</span><span class=SpellE><span class=GramE>table.xvg</span></span><span
class=GramE><span style='mso-spacerun:yes'> </span>Input</span>,
Opt.<span style='mso-spacerun:yes'> </span><span class=SpellE><span
class=GramE>xvgr/xmgr</span></span> file<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>AND NOW IT RUNS FINE, SAME TPR FILE JUST DIFFERENT DIRECTORY
…<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>SOME TIMES IT RUNS FINE IN SOME DIRECTORIES AND SOME TIME IT
DOESN’T IT’S DRIVING ME CRAZY<o:p></o:p></span></font></p>
<p class=MsoNormal><span class=GramE><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>BECAUSE I CAN’T FIGURE OUT WHY
THIS IS SO.</span></font></span><font size=2 face=Arial><span style='font-size:
10.0pt;font-family:Arial'> HALF OF MY JOBS IN THE PBS QUEUE RUN FINE, THE REST<o:p></o:p></span></font></p>
<p class=MsoNormal><span class=GramE><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>DIED OF SEGMENTATION FAULT.</span></font></span><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><span class=GramE><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>ANY CLUES?</span></font></span><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>THANKS!!!<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Claudio.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'>-----------------------------------------------------------------------------------------</span></font><span
style='mso-no-proof:yes'><o:p></o:p></span></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'>Claudio J. Margulis</span></font><span
style='mso-no-proof:yes'><o:p></o:p></span></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'>Assistant Professor</span></font><span
style='mso-no-proof:yes'><o:p></o:p></span></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'>Department of Chemistry</span></font><span
style='mso-no-proof:yes'><o:p></o:p></span></p>
<p class=MsoNormal><st1:place><st1:PlaceType><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial;mso-no-proof:yes'>University</span></font></st1:PlaceType><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial;mso-no-proof:
yes'> of </span></font><st1:PlaceName><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial;mso-no-proof:yes'>Iowa</span></font></st1:PlaceName></st1:place><span
style='mso-no-proof:yes'><o:p></o:p></span></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'>319 CB</span></font><span style='mso-no-proof:
yes'><o:p></o:p></span></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'>319-335-0615 (office)</span></font><span
style='mso-no-proof:yes'><o:p></o:p></span></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'><a
href="http://www.uiowa.edu/~chemdept/faculty/margulis/index.html">http://www.uiowa.edu/~chemdept/faculty/margulis/index.html</a></span></font><span
style='mso-no-proof:yes'><o:p></o:p></span></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'>-----------------------------------------------------------------------------------------</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
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