<html>
<head>
<style>
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Verdana
}
</style>
</head>
<body class='hmmessage'>
My *.top file is:<br><br>#include "ffoplsaa.itp"<br><br>[ moleculetype ]<br>; Name&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; nrexcl<br>CeO&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3<br><br>[ atoms ]<br>&nbsp;;&nbsp;&nbsp; nr type resnr residue&nbsp; atom cgnr charge mass<br>&nbsp;1&nbsp;&nbsp;&nbsp; opls_966&nbsp; 1&nbsp; CeO&nbsp; O&nbsp; 1&nbsp; -0.5000&nbsp; 15.9994<br>....<br>&nbsp;53&nbsp;&nbsp; opls_967&nbsp; 1&nbsp; CeO&nbsp; Ce 2&nbsp;&nbsp; 1.0000 140.116<br>....<br>[ bonds ]<br>53 1 1<br>...<br>[ angles ]<br>53 1 54 1<br>...<br><br>[ system ]<br>; Name<br>CeO<br><br>[ molecules ]<br>; Compound&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #mols<br>CeO&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 4<br><br>I do not have dihedral parameters and<br>I don not include [ pairs ] and the cutoff is 0.9 nm<br><br>Thans so much.<br><br>Osmair<br><br><br><br>&gt; Date: Thu, 28 May 2009 22:18:32 +0200<br>&gt; From: p.yamin@fz-juelich.de<br>&gt; Subject: Re: [gmx-users] Nanoparticles does not interact<br>&gt; To: gmx-users@gromacs.org<br>&gt; <br>&gt; should they really have SR interactions? what about LRs? where are they (system topology) ? do they feel each other (cutoffs) ? what do you get visualized?<br>&gt; <br>&gt; <br>&gt; <br>&gt; Peyman Yamin<br>&gt; Institut fuer Strukturbiologie und Biophysik (ISB)<br>&gt; ISB-3: Strukturbiochemie<br>&gt; Forschungszentrum Juelich<br>&gt; D-52425 Juelich <br>&gt; Tel:        (49)-2461-61-2875  <br>&gt; Fax:        (49)-2461-61-2023<br>&gt; mailto: p.yamin[at]fz-juelich.de <br>&gt; Content-Type: multipart/alternative;<br>&gt;         boundary="_501ba45b-9607-437c-8b28-bab65219d4e2_"<br>&gt; <br>&gt; <br>&gt; --_501ba45b-9607-437c-8b28-bab65219d4e2_<br>&gt; Content-Type: text/plain; charset="iso-8859-1"<br>&gt; Content-Transfer-Encoding: quoted-printable<br>&gt; <br>&gt; <br>&gt; Hi=2C<br>&gt; I have minimized four nanoparticle (with 0.5 nm of distance)<br>&gt; using the oplsaa force field=2C but the output (*.edr) shows that<br>&gt; the interactions (Coul-SR and LJ-SR) between the nanoparticles are zero=2C<br>&gt; as example:<br>&gt;        Coul-SR:1CeO-1CeO   5.84835e+04   5.43362e+09   4.45364e+06<br>&gt;          LJ-SR:1CeO-1CeO   2.26278e+00   2.10345e+05  -1.26800e+02<br>&gt;        Coul-SR:1CeO-2CeO   0.00000e+00   0.00000e+00   0.00000e+00<br>&gt;          LJ-SR:1CeO-2CeO   0.00000e+00   0.00000e+00   0.00000e+00<br>&gt;        Coul-SR:1CeO-3CeO   0.00000e+00   0.00000e+00   0.00000e+00<br>&gt;          LJ-SR:1CeO-3CeO   0.00000e+00   0.00000e+00   0.00000e+00<br>&gt;        Coul-SR:1CeO-4CeO   0.00000e+00   0.00000e+00   0.00000e+00<br>&gt;          LJ-SR:1CeO-4CeO   0.00000e+00   0.00000e+00   0.00000e+00<br>&gt;         .......<br>&gt; <br>&gt; In my *.mdp file=2C I have defined:<br>&gt; energygrps          =3D  1CeO 2CeO 3CeO 4CeO<br>&gt; <br>&gt; Someone can help me?<br>&gt; <br>&gt; Thanks<br>&gt; <br>&gt; Ph.D. Osmair V. Oliveira<br>&gt; Federal University of Sao Carlos - Brazil<br>&gt; <br>&gt; _________________________________________________________________<br>&gt; Emoticons e Winks super diferentes para o Messenger. Baixe agora=2C =E9 gr=<br>&gt; =E1tis!<br>&gt; http://specials.br.msn.com/ilovemessenger/pacotes.aspx=<br>&gt; <br>&gt; --_501ba45b-9607-437c-8b28-bab65219d4e2_<br>&gt; Content-Type: text/html; charset="iso-8859-1"<br>&gt; Content-Transfer-Encoding: quoted-printable<br>&gt; <br>&gt; &lt;html&gt;<br>&gt; &lt;head&gt;<br>&gt; &lt;style&gt;<br>&gt; .hmmessage P<br>&gt; {<br>&gt; margin:0px=3B<br>&gt; padding:0px<br>&gt; }<br>&gt; body.hmmessage<br>&gt; {<br>&gt; font-size: 10pt=3B<br>&gt; font-family:Verdana<br>&gt; }<br>&gt; &lt;/style&gt;<br>&gt; &lt;/head&gt;<br>&gt; &lt;body class=3D'hmmessage'&gt;<br>&gt; Hi=2C&lt;br&gt;I have minimized four nanoparticle (with 0.5 nm of distance)&lt;br&gt;us=<br>&gt; ing the oplsaa force field=2C but the output (*.edr) shows that&lt;br&gt;the inte=<br>&gt; ractions (Coul-SR and LJ-SR) between the nanoparticles are zero=2C&lt;br&gt;as ex=<br>&gt; ample:&lt;br&gt;&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B Coul-SR:1CeO-1Ce=<br>&gt; O&amp;nbsp=3B&amp;nbsp=3B 5.84835e+04&amp;nbsp=3B&amp;nbsp=3B 5.43362e+09&amp;nbsp=3B&amp;nbsp=3B 4=<br>&gt; .45364e+06&lt;br&gt;&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=<br>&gt; =3B LJ-SR:1CeO-1CeO&amp;nbsp=3B&amp;nbsp=3B 2.26278e+00&amp;nbsp=3B&amp;nbsp=3B 2.10345e+05=<br>&gt; &amp;nbsp=3B -1.26800e+02&lt;br&gt;&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B C=<br>&gt; oul-SR:1CeO-2CeO&amp;nbsp=3B&amp;nbsp=3B 0.00000e+00&amp;nbsp=3B&amp;nbsp=3B 0.00000e+00&amp;nb=<br>&gt; sp=3B&amp;nbsp=3B 0.00000e+00&lt;br&gt;&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=<br>&gt; =3B&amp;nbsp=3B&amp;nbsp=3B LJ-SR:1CeO-2CeO&amp;nbsp=3B&amp;nbsp=3B 0.00000e+00&amp;nbsp=3B&amp;nbs=<br>&gt; p=3B 0.00000e+00&amp;nbsp=3B&amp;nbsp=3B 0.00000e+00&lt;br&gt;&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B&amp;nb=<br>&gt; sp=3B&amp;nbsp=3B&amp;nbsp=3B Coul-SR:1CeO-3CeO&amp;nbsp=3B&amp;nbsp=3B 0.00000e+00&amp;nbsp=3B=<br>&gt; &amp;nbsp=3B 0.00000e+00&amp;nbsp=3B&amp;nbsp=3B 0.00000e+00&lt;br&gt;&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=<br>&gt; =3B&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B LJ-SR:1CeO-3CeO&amp;nbsp=3B&amp;nbsp=3B=<br>&gt;  0.00000e+00&amp;nbsp=3B&amp;nbsp=3B 0.00000e+00&amp;nbsp=3B&amp;nbsp=3B 0.00000e+00&lt;br&gt;&amp;nb=<br>&gt; sp=3B&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B Coul-SR:1CeO-4CeO&amp;nbsp=3B&amp;nbs=<br>&gt; p=3B 0.00000e+00&amp;nbsp=3B&amp;nbsp=3B 0.00000e+00&amp;nbsp=3B&amp;nbsp=3B 0.00000e+00&lt;br=<br>&gt; &gt;&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B LJ-SR:1Ce=<br>&gt; O-4CeO&amp;nbsp=3B&amp;nbsp=3B 0.00000e+00&amp;nbsp=3B&amp;nbsp=3B 0.00000e+00&amp;nbsp=3B&amp;nbsp=<br>&gt; =3B 0.00000e+00&lt;br&gt;&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B=<br>&gt;  .......&lt;br&gt;&lt;br&gt;In my *.mdp file=2C I have defined:&lt;br&gt;energygrps&amp;nbsp=3B&amp;n=<br>&gt; bsp=3B&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B&amp;nbsp=3B =3D&amp;nbsp=3B =<br>&gt; 1CeO 2CeO 3CeO 4CeO&lt;br&gt;&lt;br&gt;Someone can help me?&lt;br&gt;&lt;br&gt;Thanks&lt;br&gt;&lt;br&gt;Ph.D. =<br>&gt; Osmair V. Oliveira&lt;br&gt;Federal University of Sao Carlos - Brazil&lt;br&gt;&lt;br /&gt;&lt;h=<br>&gt; r /&gt;Quer uma internet mais segura? &lt;a href=3D'http://brasil.microsoft.com.b=<br>&gt; r/IE8/mergulhe/?utm_source=3DMSN%3BHotmail&amp;utm_medium=3DTagline&amp;utm_campaig=<br>&gt; n=3DIE8' target=3D'_new'&gt;Baixe agora o novo Internet Explorer 8. =C9 gr=E1t=<br>&gt; is!&lt;/a&gt;&lt;/body&gt;<br>&gt; &lt;/html&gt;=<br>&gt; <br>&gt; --_501ba45b-9607-437c-8b28-bab65219d4e2_--<br>&gt; <br>&gt; <br>&gt; <br>&gt; -------------------------------------------------------------------<br>&gt; -------------------------------------------------------------------<br>&gt; Forschungszentrum Juelich GmbH<br>&gt; 52425 Juelich<br>&gt; <br>&gt; Sitz der Gesellschaft: Juelich<br>&gt; Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498<br>&gt; Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe<br>&gt; Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),<br>&gt; Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt,<br>&gt; Prof. Dr. Sebastian M. Schmidt<br>&gt; -------------------------------------------------------------------<br>&gt; -------------------------------------------------------------------<br><br /><hr />Conheša os novos produtos Windows Live. <a href='http://www.windowslive.com.br' target='_new'>Clique aqui!</a></body>
</html>