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<div class=Section1>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-ansi-language:PT-BR'><span style='mso-tab-count:1'> </span><span
class=SpellE>Dear</span> <span class=SpellE>users</span>,<span
style='mso-tab-count:1'> </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;mso-ansi-language:PT-BR'><span style='mso-tab-count:1'> </span></span></font><span
class=SpellE><font size=2 face=Arial><span lang=EN-US style='font-size:10.0pt;
font-family:Arial'>I´m</span></font></span><font size=2 face=Arial><span
lang=EN-US style='font-size:10.0pt;font-family:Arial'> trying to perform 50 <span
class=SpellE>ps</span> of dynamics in an enzyme docked to its coenzyme and
cofactor but the calculation is halting in step 17 with the following message: “segmentation
fault”. <o:p></o:p></span></font></p>
<p class=MsoNormal style='text-indent:36.0pt'><font size=2 face=Arial><span
lang=EN-US style='font-size:10.0pt;font-family:Arial'>Does someone know what does
it <span class=GramE>means ?</span> I’m sending below my <span
class=SpellE>md.job</span> and <span class=SpellE>md.mdp</span> files.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><span style='mso-tab-count:1'> </span>Thanks
in advance for any help.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><span style='mso-tab-count:3'> </span><span
style='mso-spacerun:yes'> </span><b style='mso-bidi-font-weight:normal'><span
style='font-weight:bold;mso-bidi-font-weight:normal'>MD.JOB FILE<o:p></o:p></span></b></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'>Back Off! I just backed up <span
class=SpellE>mdlog.log</span> to ./#mdlog.log.1#<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><st1:City><st1:place><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;
font-family:"Courier New";mso-fareast-language:PT-BR'>Reading</span></font></st1:place></st1:City><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'> <span class=GramE>file</span> <span
class=SpellE>trp_md.tpr</span>, VERSION 3.1.4 (double precision)<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><st1:City><st1:place><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;
font-family:"Courier New";mso-fareast-language:PT-BR'>Reading</span></font></st1:place></st1:City><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'> <span class=GramE>file</span> <span
class=SpellE>trp_md.tpr</span>, VERSION 3.1.4 (double precision)<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><span
style='mso-spacerun:yes'> </span><o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'>Back Off! I just backed up <span
class=SpellE>ener.edr</span> to ./#ener.edr.2#<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=GramE><font size=2 face="Courier New"><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'>starting</span></font></span><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'> <span class=SpellE>mdrun</span> '? <span
class=GramE>in</span> water'<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=GramE><font size=2 face="Courier New"><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'>25000 steps,<span
style='mso-spacerun:yes'> </span>50.0 <span class=SpellE>ps</span>.</span></font></span><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><span
style='mso-spacerun:yes'> </span><o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><span
style='mso-spacerun:yes'> </span><o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'>Step 16, time 0.032 (<span
class=SpellE>ps</span><span class=GramE>)<span style='mso-spacerun:yes'>
</span>LINCS</span> WARNING<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=GramE><font size=2 face="Courier New"><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'>relative</span></font></span><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'> constraint deviation after LINCS:<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=GramE><font size=2 face="Courier New"><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'>max</span></font></span><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'> 10.850835 (between atoms 2168 and
2169) <span class=SpellE>rms</span> 0.243141<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=GramE><font size=2 face="Courier New"><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'>bonds</span></font></span><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'> that rotated more than 30 degrees:<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><span
style='mso-spacerun:yes'> </span><span class=GramE>atom</span> 1 atom 2<span
style='mso-spacerun:yes'> </span>angle<span style='mso-spacerun:yes'>
</span>previous, current, constraint length<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><span style='mso-spacerun:yes'>
</span>2168<span style='mso-spacerun:yes'> </span>2169<span
style='mso-spacerun:yes'> </span>90.0<span style='mso-spacerun:yes'>
</span>0.1000<span style='mso-spacerun:yes'> </span>1.1851<span
style='mso-spacerun:yes'> </span>0.1000<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><span style='mso-spacerun:yes'>
</span>9003<span style='mso-spacerun:yes'> </span>9004<span
style='mso-spacerun:yes'> </span>90.0<span style='mso-spacerun:yes'>
</span>0.1000<span style='mso-spacerun:yes'> </span>0.1783<span
style='mso-spacerun:yes'> </span>0.1000<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'>Warning: 1-4 interaction at distance
larger than 4<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'>These are ignored for the rest of the
simulation<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=GramE><font size=2 face="Courier New"><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'>turn</span></font></span><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'> on -debug for more information<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><span
style='mso-spacerun:yes'> </span><o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'>Step 17, time 0.034 (<span
class=SpellE>ps</span><span class=GramE>)<span style='mso-spacerun:yes'>
</span>LINCS</span> WARNING<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=GramE><font size=2 face="Courier New"><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'>relative</span></font></span><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'> constraint deviation after LINCS:<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=GramE><font size=2 face="Courier New"><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'>max</span></font></span><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'> 9238773122.213078 (between atoms
2168 and 2169) <span class=SpellE>rms</span> 227068560.621634<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=GramE><font size=2 face="Courier New"><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'>bonds</span></font></span><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'> that rotated more than 30 degrees:<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><span
style='mso-spacerun:yes'> </span><span class=GramE>atom</span> 1 atom 2<span
style='mso-spacerun:yes'> </span>angle<span style='mso-spacerun:yes'>
</span>previous, current, constraint length<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><span style='mso-spacerun:yes'>
</span>2164<span style='mso-spacerun:yes'> </span>2165<span
style='mso-spacerun:yes'> </span>90.0<span style='mso-spacerun:yes'>
</span>0.1000 422710940.3923<span style='mso-spacerun:yes'> </span>0.1000<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><span style='mso-spacerun:yes'>
</span>2168<span style='mso-spacerun:yes'> </span>2169<span
style='mso-spacerun:yes'> </span>90.0<span style='mso-spacerun:yes'>
</span>1.1851 923877312.3213<span style='mso-spacerun:yes'> </span>0.1000<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><span style='mso-spacerun:yes'>
</span>2436<span style='mso-spacerun:yes'> </span>2437<span
style='mso-spacerun:yes'> </span>90.0<span style='mso-spacerun:yes'>
</span>0.1000<span style='mso-spacerun:yes'> </span>1.3047<span
style='mso-spacerun:yes'> </span>0.1000<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><span style='mso-spacerun:yes'>
</span>2436<span style='mso-spacerun:yes'> </span>2438<span
style='mso-spacerun:yes'> </span>90.0<span style='mso-spacerun:yes'>
</span>0.1000<span style='mso-spacerun:yes'> </span>0.2488<span
style='mso-spacerun:yes'> </span>0.1000<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><span style='mso-spacerun:yes'>
</span>2436<span style='mso-spacerun:yes'> </span>2439<span
style='mso-spacerun:yes'> </span>90.0<span style='mso-spacerun:yes'>
</span>0.1000<span style='mso-spacerun:yes'> </span>0.6916<span
style='mso-spacerun:yes'> </span>0.1000<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><span style='mso-spacerun:yes'>
</span>9003<span style='mso-spacerun:yes'> </span>9004<span
style='mso-spacerun:yes'> </span>90.0<span style='mso-spacerun:yes'>
</span>0.1783<span style='mso-spacerun:yes'> </span>0.3997<span
style='mso-spacerun:yes'> </span>0.1000<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><span style='mso-spacerun:yes'>
</span>9095<span style='mso-spacerun:yes'> </span>9096<span
style='mso-spacerun:yes'> </span>31.6<span style='mso-spacerun:yes'>
</span>0.1000<span style='mso-spacerun:yes'> </span><span class=SpellE>0.1000</span><span
style='mso-spacerun:yes'> </span><span class=SpellE>0.1000</span><o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'>[3]<span class=GramE>+<span
style='mso-spacerun:yes'> </span>Segmentation</span> fault<span
style='mso-spacerun:yes'> </span><span class=SpellE>mdrun_d</span> -s <span
class=SpellE>trp_md.tpr</span> -o <span class=SpellE>trp_md.trr</span> -c
trp_b4md.gro -g <span class=SpellE>mdlog</span> 1>&<span class=SpellE>md.job</span><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><span style='mso-tab-count:4'> </span><span
style='mso-spacerun:yes'> </span><span
style='mso-spacerun:yes'> </span><b style='mso-bidi-font-weight:normal'><span
style='font-weight:bold;mso-bidi-font-weight:normal'>MD.MDP FILE<o:p></o:p></span></b></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'>;<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'>;<span style='mso-tab-count:1'> </span>User
<span class=SpellE>spoel</span> (236)<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'>;<span style='mso-tab-count:1'> </span>Wed
<span class=GramE>Nov<span style='mso-spacerun:yes'> </span>3</span> 17:12:44
1993<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'>;<span style='mso-tab-count:1'> </span>Input
file<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=GramE><font size=2 face="Courier New"><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'>title</span></font></span><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><span
style='mso-spacerun:yes'> </span>=<span
style='mso-spacerun:yes'> </span>PEP MD<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span class=GramE><font size=2 face="Courier New"><span
lang=EN-US style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:
PT-BR'>cpp</span></font></span></span><font size=2 face="Courier New"><span
lang=EN-US style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:
PT-BR'><span style='mso-spacerun:yes'> </span>=<span
style='mso-spacerun:yes'> </span>/lib/<span class=SpellE>cpp</span><o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=GramE><font size=2 face="Courier New"><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'>define</span></font></span><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><span
style='mso-spacerun:yes'> </span>=<span style='mso-spacerun:yes'>
</span>-DFLEX_SPC<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=GramE><font size=2 face="Courier New"><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'>constraints</span></font></span><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><span
style='mso-spacerun:yes'> </span>=<span style='mso-spacerun:yes'>
</span><span class=SpellE>hbonds</span><o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=GramE><font size=2 face="Courier New"><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'>integrator</span></font></span><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><span
style='mso-spacerun:yes'> </span>=<span style='mso-spacerun:yes'>
</span><span class=SpellE>md</span><o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span class=GramE><font size=2 face="Courier New"><span
lang=EN-US style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:
PT-BR'>dt</span></font></span></span><font size=2 face="Courier New"><span
lang=EN-US style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:
PT-BR'><span style='mso-spacerun:yes'> </span>=<span
style='mso-spacerun:yes'> </span>0.002<span style='mso-spacerun:yes'>
</span>; <span class=SpellE>ps</span> !<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span class=GramE><font size=2 face="Courier New"><span
lang=EN-US style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:
PT-BR'>nsteps</span></font></span></span><font size=2 face="Courier New"><span
lang=EN-US style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:
PT-BR'><span style='mso-spacerun:yes'> </span>=<span
style='mso-spacerun:yes'> </span>25000<span style='mso-spacerun:yes'>
</span>; total 50ps<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span class=GramE><font size=2 face="Courier New"><span
lang=EN-US style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:
PT-BR'>nstcomm</span></font></span></span><font size=2 face="Courier New"><span
lang=EN-US style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:
PT-BR'><span style='mso-spacerun:yes'> </span>=<span
style='mso-spacerun:yes'> </span>1<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span class=GramE><font size=2 face="Courier New"><span
lang=EN-US style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:
PT-BR'>nstxout</span></font></span></span><font size=2 face="Courier New"><span
lang=EN-US style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:
PT-BR'><span style='mso-spacerun:yes'> </span>=<span
style='mso-spacerun:yes'> </span>500<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span class=GramE><font size=2 face="Courier New"><span
lang=EN-US style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:
PT-BR'>nstvout</span></font></span></span><font size=2 face="Courier New"><span
lang=EN-US style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:
PT-BR'><span style='mso-spacerun:yes'> </span>=<span
style='mso-spacerun:yes'> </span>0<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span class=GramE><font size=2 face="Courier New"><span
lang=EN-US style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:
PT-BR'>nstfout</span></font></span></span><font size=2 face="Courier New"><span
lang=EN-US style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:
PT-BR'><span style='mso-spacerun:yes'> </span>=<span
style='mso-spacerun:yes'> </span>0<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span class=GramE><font size=2 face="Courier New"><span
lang=EN-US style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:
PT-BR'>nstlist</span></font></span></span><font size=2 face="Courier New"><span
lang=EN-US style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:
PT-BR'><span style='mso-spacerun:yes'> </span>=<span
style='mso-spacerun:yes'> </span>5<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><font size=2 face="Courier New"><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'>ns_type</span></font></span><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><span
style='mso-spacerun:yes'> </span><span class=GramE>=<span
style='mso-spacerun:yes'> </span>grid</span><o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span class=GramE><font size=2 face="Courier New"><span
lang=EN-US style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:
PT-BR'>rlist</span></font></span></span><font size=2 face="Courier New"><span
lang=EN-US style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:
PT-BR'><span style='mso-spacerun:yes'> </span>=<span
style='mso-spacerun:yes'> </span>0.9<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span class=GramE><font size=2 face="Courier New"><span
lang=EN-US style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:
PT-BR'>coulombtype</span></font></span></span><font size=2 face="Courier New"><span
lang=EN-US style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:
PT-BR'><span style='mso-spacerun:yes'> </span>=<span
style='mso-spacerun:yes'> </span>PME<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span class=GramE><font size=2 face="Courier New"><span
lang=EN-US style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:
PT-BR'>rcoulomb</span></font></span></span><font size=2 face="Courier New"><span
lang=EN-US style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:
PT-BR'><span style='mso-spacerun:yes'> </span>=<span
style='mso-spacerun:yes'> </span>0.9<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span class=GramE><font size=2 face="Courier New"><span
lang=EN-US style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:
PT-BR'>rvdw</span></font></span></span><font size=2 face="Courier New"><span
lang=EN-US style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:
PT-BR'><span style='mso-spacerun:yes'> </span>=<span
style='mso-spacerun:yes'> </span>0.9<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><font size=2 face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New";mso-ansi-language:PT-BR;mso-fareast-language:PT-BR'>fourierspacing</span></font></span><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New";
mso-ansi-language:PT-BR;mso-fareast-language:PT-BR'><span
style='mso-spacerun:yes'> </span>=<span style='mso-spacerun:yes'>
</span>0.12<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><font size=2 face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New";mso-ansi-language:PT-BR;mso-fareast-language:PT-BR'>fourier_nx</span></font></span><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New";
mso-ansi-language:PT-BR;mso-fareast-language:PT-BR'><span
style='mso-spacerun:yes'> </span>=<span style='mso-spacerun:yes'>
</span>0<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><font size=2 face="Courier New"><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'>fourier_ny</span></font></span><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><span
style='mso-spacerun:yes'> </span><span class=GramE>=<span
style='mso-spacerun:yes'> </span>0</span><o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><font size=2 face="Courier New"><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'>fourier_nz</span></font></span><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><span
style='mso-spacerun:yes'> </span><span class=GramE>=<span
style='mso-spacerun:yes'> </span>0</span><o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><font size=2 face="Courier New"><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'>pme_order</span></font></span><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><span
style='mso-spacerun:yes'> </span><span class=GramE>=<span
style='mso-spacerun:yes'> </span>4</span><o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><font size=2 face="Courier New"><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'>ewald_rtol</span></font></span><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><span
style='mso-spacerun:yes'> </span><span class=GramE>=<span
style='mso-spacerun:yes'> </span>1e</span>-5<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><font size=2 face="Courier New"><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'>optimize_fft</span></font></span><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><span
style='mso-spacerun:yes'> </span><span class=GramE>=<span
style='mso-spacerun:yes'> </span>yes</span><o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'>; <span class=SpellE>Berendsen</span>
temperature coupling is on in three groups<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><font size=2 face="Courier New"><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'>Tcoupl</span></font></span><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><span
style='mso-spacerun:yes'> </span><span class=GramE>=<span
style='mso-spacerun:yes'> </span><span class=SpellE>Berendsen</span></span><o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><font size=2 face="Courier New"><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'>tau_t</span></font></span><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><span
style='mso-spacerun:yes'> </span>= 0.1<span
style='mso-spacerun:yes'> </span><span class=SpellE>0.1</span><span
style='mso-spacerun:yes'> </span><span class=SpellE>0.1</span><o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span class=GramE><font size=2 face="Courier New"><span
lang=EN-US style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:
PT-BR'>tc-grps</span></font></span></span><font size=2 face="Courier New"><span
lang=EN-US style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:
PT-BR'><span style='mso-spacerun:yes'> </span>= protein<span
style='mso-spacerun:yes'> </span><span class=SpellE>drg</span><span
style='mso-spacerun:yes'> </span>sol<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><font size=2 face="Courier New"><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'>ref_t</span></font></span><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><span
style='mso-spacerun:yes'> </span>= 300<span
style='mso-spacerun:yes'> </span><span class=SpellE>300</span><span
style='mso-spacerun:yes'> </span><span class=SpellE>300</span><o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'>; Pressure coupling is not on<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><font size=2 face="Courier New"><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'>Pcoupl</span></font></span><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><span style='mso-spacerun:yes'>
</span><span style='mso-spacerun:yes'> </span>= no<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span class=GramE><font size=2 face="Courier New"><span
lang=EN-US style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:
PT-BR'>pcoupltype</span></font></span></span><font size=2 face="Courier New"><span
lang=EN-US style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:
PT-BR'><span style='mso-spacerun:yes'> </span>= isotropic<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><font size=2 face="Courier New"><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'>tau_p</span></font></span><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><span
style='mso-spacerun:yes'> </span>= 0.5<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=GramE><font size=2 face="Courier New"><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'>compressibility</span></font></span><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><span style='mso-spacerun:yes'>
</span>= 4.5e-5<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><font size=2 face="Courier New"><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'>ref_p</span></font></span><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><span
style='mso-spacerun:yes'> </span>= 1.0<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'>; Generate velocities is on at 300 K<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><font size=2 face="Courier New"><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'>gen_vel</span></font></span><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><span
style='mso-spacerun:yes'> </span>= yes<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><font size=2 face="Courier New"><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'>gen_temp</span></font></span><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><span
style='mso-spacerun:yes'> </span>= 300.0<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><font size=2 face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New";mso-ansi-language:PT-BR;mso-fareast-language:PT-BR'>gen_seed</span></font></span><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New";
mso-ansi-language:PT-BR;mso-fareast-language:PT-BR'><span
style='mso-spacerun:yes'> </span>= 173529<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
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