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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"><meta http-equiv="Content-Type" content="text/html; charset=utf-8"><meta name="ProgId" content="Word.Document"><meta name="Generator" content="Microsoft Word 12"><meta name="Originator" content="Microsoft Word 12"><link rel="File-List" href="file:///C:%5CDOCUME%7E1%5CDEAR-U%7E1%5CLOCALS%7E1%5CTemp%5Cmsohtmlclip1%5C01%5Cclip_filelist.xml"><link rel="themeData" href="file:///C:%5CDOCUME%7E1%5CDEAR-U%7E1%5CLOCALS%7E1%5CTemp%5Cmsohtmlclip1%5C01%5Cclip_themedata.thmx"><link rel="colorSchemeMapping" href="file:///C:%5CDOCUME%7E1%5CDEAR-U%7E1%5CLOCALS%7E1%5CTemp%5Cmsohtmlclip1%5C01%5Cclip_colorschememapping.xml"><style>
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</p><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 name="OLE_LINK4"></a><a 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><meta http-equiv="Content-Type" content="text/html; charset=utf-8"><meta name="ProgId" content="Word.Document"><meta name="Generator" content="Microsoft Word 12"><meta name="Originator" content="Microsoft Word 12"><link rel="File-List" href="file:///C:%5CDOCUME%7E1%5CDEAR-U%7E1%5CLOCALS%7E1%5CTemp%5Cmsohtmlclip1%5C01%5Cclip_filelist.xml"><link rel="themeData" href="file:///C:%5CDOCUME%7E1%5CDEAR-U%7E1%5CLOCALS%7E1%5CTemp%5Cmsohtmlclip1%5C01%5Cclip_themedata.thmx"><link rel="colorSchemeMapping" href="file:///C:%5CDOCUME%7E1%5CDEAR-U%7E1%5CLOCALS%7E1%5CTemp%5Cmsohtmlclip1%5C01%5Cclip_colorschememapping.xml"><style>
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</style><span dir="ltr"><span style=""> </span></span><span dir="ltr" style="font-size: 10pt; line-height: 115%; font-family: "Tahoma","sans-serif";"><br></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><p></p>