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My *.top file is:<br><br>#include "ffoplsaa.itp"<br><br>[ moleculetype ]<br>; Name nrexcl<br>CeO 3<br><br>[ atoms ]<br> ; nr type resnr residue atom cgnr charge mass<br> 1 opls_966 1 CeO O 1 -0.5000 15.9994<br>....<br> 53 opls_967 1 CeO Ce 2 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 #mols<br>CeO 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>> Date: Thu, 28 May 2009 22:18:32 +0200<br>> From: p.yamin@fz-juelich.de<br>> Subject: Re: [gmx-users] Nanoparticles does not interact<br>> To: gmx-users@gromacs.org<br>> <br>> 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>> <br>> <br>> <br>> Peyman Yamin<br>> Institut fuer Strukturbiologie und Biophysik (ISB)<br>> ISB-3: Strukturbiochemie<br>> Forschungszentrum Juelich<br>> D-52425 Juelich <br>> Tel: (49)-2461-61-2875 <br>> Fax: (49)-2461-61-2023<br>> mailto: p.yamin[at]fz-juelich.de <br>> Content-Type: multipart/alternative;<br>> boundary="_501ba45b-9607-437c-8b28-bab65219d4e2_"<br>> <br>> <br>> --_501ba45b-9607-437c-8b28-bab65219d4e2_<br>> Content-Type: text/plain; charset="iso-8859-1"<br>> Content-Transfer-Encoding: quoted-printable<br>> <br>> <br>> Hi=2C<br>> I have minimized four nanoparticle (with 0.5 nm of distance)<br>> using the oplsaa force field=2C but the output (*.edr) shows that<br>> the interactions (Coul-SR and LJ-SR) between the nanoparticles are zero=2C<br>> as example:<br>> Coul-SR:1CeO-1CeO 5.84835e+04 5.43362e+09 4.45364e+06<br>> LJ-SR:1CeO-1CeO 2.26278e+00 2.10345e+05 -1.26800e+02<br>> Coul-SR:1CeO-2CeO 0.00000e+00 0.00000e+00 0.00000e+00<br>> LJ-SR:1CeO-2CeO 0.00000e+00 0.00000e+00 0.00000e+00<br>> Coul-SR:1CeO-3CeO 0.00000e+00 0.00000e+00 0.00000e+00<br>> LJ-SR:1CeO-3CeO 0.00000e+00 0.00000e+00 0.00000e+00<br>> Coul-SR:1CeO-4CeO 0.00000e+00 0.00000e+00 0.00000e+00<br>> LJ-SR:1CeO-4CeO 0.00000e+00 0.00000e+00 0.00000e+00<br>> .......<br>> <br>> In my *.mdp file=2C I have defined:<br>> energygrps =3D 1CeO 2CeO 3CeO 4CeO<br>> <br>> Someone can help me?<br>> <br>> Thanks<br>> <br>> Ph.D. Osmair V. Oliveira<br>> Federal University of Sao Carlos - Brazil<br>> <br>> _________________________________________________________________<br>> Emoticons e Winks super diferentes para o Messenger. Baixe agora=2C =E9 gr=<br>> =E1tis!<br>> http://specials.br.msn.com/ilovemessenger/pacotes.aspx=<br>> <br>> --_501ba45b-9607-437c-8b28-bab65219d4e2_<br>> Content-Type: text/html; charset="iso-8859-1"<br>> Content-Transfer-Encoding: quoted-printable<br>> <br>> <html><br>> <head><br>> <style><br>> .hmmessage P<br>> {<br>> margin:0px=3B<br>> padding:0px<br>> }<br>> body.hmmessage<br>> {<br>> font-size: 10pt=3B<br>> font-family:Verdana<br>> }<br>> </style><br>> </head><br>> <body class=3D'hmmessage'><br>> Hi=2C<br>I have minimized four nanoparticle (with 0.5 nm of distance)<br>us=<br>> ing the oplsaa force field=2C but the output (*.edr) shows that<br>the inte=<br>> ractions (Coul-SR and LJ-SR) between the nanoparticles are zero=2C<br>as ex=<br>> ample:<br>&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B Coul-SR:1CeO-1Ce=<br>> O&nbsp=3B&nbsp=3B 5.84835e+04&nbsp=3B&nbsp=3B 5.43362e+09&nbsp=3B&nbsp=3B 4=<br>> .45364e+06<br>&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=<br>> =3B LJ-SR:1CeO-1CeO&nbsp=3B&nbsp=3B 2.26278e+00&nbsp=3B&nbsp=3B 2.10345e+05=<br>> &nbsp=3B -1.26800e+02<br>&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B C=<br>> oul-SR:1CeO-2CeO&nbsp=3B&nbsp=3B 0.00000e+00&nbsp=3B&nbsp=3B 0.00000e+00&nb=<br>> sp=3B&nbsp=3B 0.00000e+00<br>&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=<br>> =3B&nbsp=3B&nbsp=3B LJ-SR:1CeO-2CeO&nbsp=3B&nbsp=3B 0.00000e+00&nbsp=3B&nbs=<br>> p=3B 0.00000e+00&nbsp=3B&nbsp=3B 0.00000e+00<br>&nbsp=3B&nbsp=3B&nbsp=3B&nb=<br>> sp=3B&nbsp=3B&nbsp=3B Coul-SR:1CeO-3CeO&nbsp=3B&nbsp=3B 0.00000e+00&nbsp=3B=<br>> &nbsp=3B 0.00000e+00&nbsp=3B&nbsp=3B 0.00000e+00<br>&nbsp=3B&nbsp=3B&nbsp=<br>> =3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B LJ-SR:1CeO-3CeO&nbsp=3B&nbsp=3B=<br>> 0.00000e+00&nbsp=3B&nbsp=3B 0.00000e+00&nbsp=3B&nbsp=3B 0.00000e+00<br>&nb=<br>> sp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B Coul-SR:1CeO-4CeO&nbsp=3B&nbs=<br>> p=3B 0.00000e+00&nbsp=3B&nbsp=3B 0.00000e+00&nbsp=3B&nbsp=3B 0.00000e+00<br=<br>> >&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B LJ-SR:1Ce=<br>> O-4CeO&nbsp=3B&nbsp=3B 0.00000e+00&nbsp=3B&nbsp=3B 0.00000e+00&nbsp=3B&nbsp=<br>> =3B 0.00000e+00<br>&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B=<br>> .......<br><br>In my *.mdp file=2C I have defined:<br>energygrps&nbsp=3B&n=<br>> bsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B =3D&nbsp=3B =<br>> 1CeO 2CeO 3CeO 4CeO<br><br>Someone can help me?<br><br>Thanks<br><br>Ph.D. =<br>> Osmair V. 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