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<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'>Dear Sir or Madam:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'><span
style='mso-spacerun:yes'> </span>I am trying to simulate
the interface between alkyls & water, the <span class=SpellE>decane</span>
(<span class=GramE>C10 ,</span> declared in <span class=SpellE>ffgmx.itp</span>)
and SOL (OPLS) are used. <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'>But I’ve met some
problems:<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-indent:21.0pt'><font size=1 face=Arial><span
lang=EN-US style='font-size:9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'>1.
<span class=SpellE><span class=GramE>mdrun</span></span> always throw some
error message, then <span class=SpellE>stoped</span><o:p></o:p></span></font></p>
<p class=MsoNormal style='text-indent:21.0pt'><font size=1 face=Arial><span
lang=EN-US style='font-size:9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'>2.
<span class=GramE>how</span> to enlarge “energy minimize “ step
length? I’d modified the “<span class=SpellE>emstep</span> “,
but the <span class=SpellE>mdrun</span> <span class=SpellE>shinked</span> it
rapidly.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'>Could you please give me
some advice?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'>Thank you very much in
advance!<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><span class=SpellE><span class=GramE><font size=1
face=Arial><span lang=EN-US style='font-size:9.0pt;mso-bidi-font-size:10.0pt;
font-family:Arial'>rayn</span></font></span></span><font size=1 face=Arial><span
lang=EN-US style='font-size:9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'>Step 0, time 0 (<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><span class=GramE><font size=1 face=Arial><span lang=EN-US
style='font-size:9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'>relative</span></font></span><font
size=1 face=Arial><span lang=EN-US style='font-size:9.0pt;mso-bidi-font-size:
10.0pt;font-family:Arial'> constraint deviation after LINCS:<o:p></o:p></span></font></p>
<p class=MsoNormal><span class=GramE><font size=1 face=Arial><span lang=EN-US
style='font-size:9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'>max</span></font></span><font
size=1 face=Arial><span lang=EN-US style='font-size:9.0pt;mso-bidi-font-size:
10.0pt;font-family:Arial'> 40.729252 (between atoms 1854 and 1855) <span
class=SpellE>rms</span> 1.751049<o:p></o:p></span></font></p>
<p class=MsoNormal><span class=GramE><font size=1 face=Arial><span lang=EN-US
style='font-size:9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'>bonds</span></font></span><font
size=1 face=Arial><span lang=EN-US style='font-size:9.0pt;mso-bidi-font-size:
10.0pt;font-family:Arial'> that rotated more than 30 degrees:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'><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><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'><span
style='mso-spacerun:yes'> </span>391<span
style='mso-spacerun:yes'> </span>392<span
style='mso-spacerun:yes'> </span>46.6<span
style='mso-spacerun:yes'> </span>0.1530<span
style='mso-spacerun:yes'> </span>0.1549<span
style='mso-spacerun:yes'> </span>0.1530<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'><span
style='mso-spacerun:yes'> </span>392<span
style='mso-spacerun:yes'> </span>393<span
style='mso-spacerun:yes'> </span>45.9<span
style='mso-spacerun:yes'> </span>0.1530<span
style='mso-spacerun:yes'> </span>0.1517<span
style='mso-spacerun:yes'> </span>0.1530<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'><span
style='mso-spacerun:yes'> </span>738<span
style='mso-spacerun:yes'> </span>739<span
style='mso-spacerun:yes'> </span>35.7<span
style='mso-spacerun:yes'> </span>0.1530<span
style='mso-spacerun:yes'> </span>0.1851<span
style='mso-spacerun:yes'> </span>0.1530<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'><span
style='mso-spacerun:yes'> </span>739<span
style='mso-spacerun:yes'> </span>740<span
style='mso-spacerun:yes'> </span>90.0<span
style='mso-spacerun:yes'> </span>0.1530<span
style='mso-spacerun:yes'> </span>0.1464<span
style='mso-spacerun:yes'> </span>0.1530<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'><span
style='mso-spacerun:yes'> </span>1245<span
style='mso-spacerun:yes'> </span>1246<span
style='mso-spacerun:yes'> </span>35.2<span
style='mso-spacerun:yes'> </span>0.1530<span
style='mso-spacerun:yes'> </span>0.1874<span
style='mso-spacerun:yes'> </span>0.1530<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'>………….<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'>My <span class=SpellE><span
class=GramE>em.mdp</span></span><span class=GramE> :</span> <o:p></o:p></span></font></p>
<p class=MsoNormal><span class=GramE><font size=1 face=Arial><span lang=EN-US
style='font-size:9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'>constraints</span></font></span><font
size=1 face=Arial><span lang=EN-US style='font-size:9.0pt;mso-bidi-font-size:
10.0pt;font-family:Arial'><span
style='mso-spacerun:yes'>
</span>=<span style='mso-spacerun:yes'> </span>none<o:p></o:p></span></font></p>
<p class=MsoNormal><span class=GramE><font size=1 face=Arial><span lang=EN-US
style='font-size:9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'>integrator</span></font></span><font
size=1 face=Arial><span lang=EN-US style='font-size:9.0pt;mso-bidi-font-size:
10.0pt;font-family:Arial'><span
style='mso-spacerun:yes'>
</span>=<span style='mso-spacerun:yes'> </span>steep<o:p></o:p></span></font></p>
<p class=MsoNormal><span class=SpellE><span class=GramE><font size=1
face=Arial><span lang=EN-US style='font-size:9.0pt;mso-bidi-font-size:10.0pt;
font-family:Arial'>dt</span></font></span></span><font size=1 face=Arial><span
lang=EN-US style='font-size:9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'><span
style='mso-spacerun:yes'>
</span>=<span style='mso-spacerun:yes'> </span>0.0001<span
style='mso-spacerun:yes'> </span><o:p></o:p></span></font></p>
<p class=MsoNormal><span class=SpellE><span class=GramE><font size=1
face=Arial><span lang=EN-US style='font-size:9.0pt;mso-bidi-font-size:10.0pt;
font-family:Arial'>nsteps</span></font></span></span><font size=1 face=Arial><span
lang=EN-US style='font-size:9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'><span
style='mso-spacerun:yes'>
</span>=<span style='mso-spacerun:yes'> </span>5000<span
style='mso-tab-count:1'> </span><o:p></o:p></span></font></p>
<p class=MsoNormal><span class=SpellE><span class=GramE><font size=1
face=Arial><span lang=EN-US style='font-size:9.0pt;mso-bidi-font-size:10.0pt;
font-family:Arial'>nstlist</span></font></span></span><font size=1 face=Arial><span
lang=EN-US style='font-size:9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'><span
style='mso-spacerun:yes'>
</span>=<span style='mso-spacerun:yes'> </span>0<o:p></o:p></span></font></p>
<p class=MsoNormal><span class=SpellE><font size=1 face=Arial><span lang=EN-US
style='font-size:9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'>ns_type</span></font></span><font
size=1 face=Arial><span lang=EN-US style='font-size:9.0pt;mso-bidi-font-size:
10.0pt;font-family:Arial'><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><span class=SpellE><span class=GramE><font size=1
face=Arial><span lang=EN-US style='font-size:9.0pt;mso-bidi-font-size:10.0pt;
font-family:Arial'>rlist</span></font></span></span><font size=1 face=Arial><span
lang=EN-US style='font-size:9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'><span
style='mso-spacerun:yes'>
</span>=<span style='mso-spacerun:yes'> </span>1.0<o:p></o:p></span></font></p>
<p class=MsoNormal><span class=SpellE><span class=GramE><font size=1
face=Arial><span lang=EN-US style='font-size:9.0pt;mso-bidi-font-size:10.0pt;
font-family:Arial'>rcoulomb</span></font></span></span><font size=1 face=Arial><span
lang=EN-US style='font-size:9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'><span
style='mso-spacerun:yes'>
</span>=<span style='mso-spacerun:yes'> </span>1.0<o:p></o:p></span></font></p>
<p class=MsoNormal><span class=SpellE><span class=GramE><font size=1
face=Arial><span lang=EN-US style='font-size:9.0pt;mso-bidi-font-size:10.0pt;
font-family:Arial'>rvdw</span></font></span></span><font size=1 face=Arial><span
lang=EN-US style='font-size:9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'><span
style='mso-spacerun:yes'>
</span><span
style='mso-spacerun:yes'> </span>=<span
style='mso-spacerun:yes'> </span>1.0<o:p></o:p></span></font></p>
<p class=MsoNormal><span class=SpellE><span class=GramE><font size=1
face=Arial><span lang=EN-US style='font-size:9.0pt;mso-bidi-font-size:10.0pt;
font-family:Arial'>emtol</span></font></span></span><font size=1 face=Arial><span
lang=EN-US style='font-size:9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'><span
style='mso-spacerun:yes'>
</span>=<span style='mso-spacerun:yes'> </span>10.0<span
style='mso-tab-count:1'> </span><o:p></o:p></span></font></p>
<p class=MsoNormal><span class=SpellE><span class=GramE><font size=1
face=Arial><span lang=EN-US style='font-size:9.0pt;mso-bidi-font-size:10.0pt;
font-family:Arial'>emstep</span></font></span></span><font size=1 face=Arial><span
lang=EN-US style='font-size:9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'><span
style='mso-spacerun:yes'>
</span>=<span style='mso-spacerun:yes'> </span>0.5<o:p></o:p></span></font></p>
<p class=MsoNormal><span class=SpellE><span class=GramE><font size=1
face=Arial><span lang=EN-US style='font-size:9.0pt;mso-bidi-font-size:10.0pt;
font-family:Arial'>nstcgsteep</span></font></span></span><font size=1
face=Arial><span lang=EN-US style='font-size:9.0pt;mso-bidi-font-size:10.0pt;
font-family:Arial'><span
style='mso-spacerun:yes'>
</span>=<span style='mso-spacerun:yes'> </span>100<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;mso-bidi-font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
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