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On 9/07/2010 2:16 PM, jasmine wrote:
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<p class="MsoNormal" dir="rtl" style="text-align: left;" align="right"><span
dir="ltr">Hi
everyone;</span></p>
<p class="MsoNormal" dir="rtl" style="text-align: left;" align="right">
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<p class="MsoNormal" dir="rtl" style="text-align: left;" align="right"><span
dir="ltr">I
am simulating a functionalized nanotube with (CH3) group .the nanotube
atoms
are uncharged and rigid but<span style=""> </span>the atoms of
<span style=""> </span>(CH3) group are charged <span style=""> </span>and
flexible<span style="">
</span>,and <span style=""> </span>are defined in the residue
name of [atom]<span style=""> </span>section of <span style=""> </span>topology
file with (CNT)and (FUNC) , Respectively.
I have decided to freeze my<span style=""> </span>CNT<span style="">
</span>in all 3 directions. In fact , I have
flexible group anchored to a <span style=""> </span>frozen
surface of CNT . thus , I used <span style=""> </span>(<a
moz-do-not-send="true" name="OLE_LINK4"></a><a moz-do-not-send="true"
name="OLE_LINK3"><span style="">energygrp_exl
= CNT<span style=""> </span>CNT</span></a><span style=""> </span><span
style=""> </span>,<span style=""> </span><span style=""> </span>freezegrps
<span style=""> </span>= CNT<span style="">
</span>,<span style=""> </span>coulombtype <span style=""> </span>=
PME<span style=""> </span>)
,but I get the following warning upon running grompp.</span></p>
<p class="MsoNormal" dir="rtl" style="text-align: left;" align="right"><span
dir="ltr">Can
not exclude the lattice coulomb energy between energy groups</span></p>
<p class="MsoNormal" dir="rtl" style="text-align: left;" align="right"><span
dir="ltr">Please
correct my <span style=""> </span>.mdp file and add any</span><span
dir="ltr"
style="font-size: 10pt; line-height: 115%; font-family: "Tahoma","sans-serif";">
requisite</span><span dir="ltr"> </span><span dir="ltr">option </span><span
dir="ltr"
style="font-size: 10pt; line-height: 115%; font-family: "Tahoma","sans-serif";">
in this p case.</span><span dir="ltr"> </span>
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</span><span dir="ltr"></span><span dir="ltr"
style="font-size: 10pt; line-height: 115%; font-family: "Tahoma","sans-serif";"></span></p>
<p class="MsoNormal" dir="rtl" style="text-align: left;" align="right"><span
dir="ltr">coulombtype<span style=""> </span><span style=""> </span>=
PME</span></p>
<p class="MsoNormal" dir="rtl" style="text-align: left;" align="right"><span
dir="ltr">energygrps<span style=""> </span><span style=""> </span>=
CNT
<span style=""> </span>FUNC</span></p>
<p class="MsoNormal" dir="rtl" style="text-align: left;" align="right"><span
dir="ltr">constraints<span style=""> </span><span style=""> </span>=
none</span></p>
<p class="MsoNormal" dir="rtl" style="text-align: left;" align="right"><span
dir="ltr">energygrp_excl
<span style=""> </span>= CNT <span style=""> </span>CNT</span></p>
<p class="MsoNormal" dir="rtl" style="text-align: left;" align="right"><span
dir="ltr">freezegrps
<span style=""> </span>= CNT <span style=""> </span></span><span
style="font-family: "Arial","sans-serif";" lang="FA"></span></p>
<p class="MsoNormal" dir="rtl" style="text-align: left;" align="right"><span
dir="ltr">freezedim<span style=""> </span><span style=""> </span>=
Y Y
Y</span></p>
<span
style="font-size: 11pt; line-height: 115%; font-family: "Calibri","sans-serif";">Thank
you</span>
</blockquote>
PME and energy exclusions are mutually incompatible. That's intrinisic
to how PME works.<br>
<br>
Mark<br>
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