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Hi Mark,<br><br>My *.mdp file:<br>cpp = /lib/cpp<br>integrator = md<br>;constraints = h-bonds<br>dt = 0.001<br>nsteps = 5000000<br>nstcomm = 1<br>nstxout = 1000<br>nstvout = 1000<br>nstxtcout = 100<br>nstlog = 1000<br>nstenergy = 100<br>nstlist = 10<br>pbc = xyz<br>ns_type = grid<br>rlist = 1.0<br>rvdw = 1.0<br>rcoulomb = 1.0<br>coulombtype = pme <br>fourierspacing = 0.12<br>pme_order = 4<br>energygrps = SOL 1CeO 2CeO 3CeO 4CeO <br>Tcoupl = berendsen<br>tc-grps = system <br>ref_t = 298 <br>tau_t = 0.1<br>pcoupl = berendsen<br>tau_p = 10.0<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>gen_vel = no<br><br>About clarifying "I have minimized four nanoparticle (with 0.5 nm of distance)".<br>I build my system inseting four nanoparticles into a box with 7,000 water molecules.<br>The initial distance between the nanoparticles are 0.5 nm. After 5 ns of simulation<br>(using the *.mdp file above), this distance is 0.3 nm, sufficiently for interactions<br>between the nanoparticles. However, these interactions (Coulomb and LJ) are zero.<br>On the other hand, there are interactions between nanoparticle-water and <br>nanoparticle intramolecular. <br><br>I hope that this can help.<br><br>Thanks so much,<br>Osmair<br> <br><br>> Date: Fri, 29 May 2009 12:12:34 +1000<br>> From: Mark.Abraham@anu.edu.au<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Nanoparticles does not interact<br>> <br>> osmair oliveira wrote:<br>> > 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>> Including your .mdp file and clarifying "I have minimized four <br>> nanoparticle (with 0.5 nm of distance)" would be helpful. Are there <br>> atoms in difference particles whose interaction distances are inside <br>> your cutoffs?<br>> <br>> Mark<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 <br>> > they (system topology) ? do they feel each other (cutoffs) ? what do you <br>> > 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 <br>> > 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 <br>> > =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 <br>> > distance)<br>us=<br>> > > ing the oplsaa force field=2C but the output (*.edr) shows <br>> > that<br>the inte=<br>> > > ractions (Coul-SR and LJ-SR) between the nanoparticles are <br>> > zero=2C<br>as ex=<br>> > > ample:<br>&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B <br>> > Coul-SR:1CeO-1Ce=<br>> > > O&nbsp=3B&nbsp=3B 5.84835e+04&nbsp=3B&nbsp=3B <br>> > 5.43362e+09&nbsp=3B&nbsp=3B 4=<br>> > > <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 <br>> > 2.10345e+05=<br>> > > &nbsp=3B <br>> > -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 <br>> > 0.00000e+00&nb=<br>> > > sp=3B&nbsp=3B <br>> > 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 <br>> > 0.00000e+00&nbsp=3B&nbs=<br>> > > p=3B 0.00000e+00&nbsp=3B&nbsp=3B <br>> > 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 <br>> > 0.00000e+00&nbsp=3B=<br>> > > &nbsp=3B 0.00000e+00&nbsp=3B&nbsp=3B <br>> > 0.00000e+00<br>&nbsp=3B&nbsp=3B&nbsp=<br>> > > =3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B <br>> > LJ-SR:1CeO-3CeO&nbsp=3B&nbsp=3B=<br>> > > 0.00000e+00&nbsp=3B&nbsp=3B 0.00000e+00&nbsp=3B&nbsp=3B <br>> > 0.00000e+00<br>&nb=<br>> > > sp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B <br>> > Coul-SR:1CeO-4CeO&nbsp=3B&nbs=<br>> > > p=3B 0.00000e+00&nbsp=3B&nbsp=3B 0.00000e+00&nbsp=3B&nbsp=3B <br>> > 0.00000e+00<br=<br>> > > >&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B <br>> > LJ-SR:1Ce=<br>> > > O-4CeO&nbsp=3B&nbsp=3B 0.00000e+00&nbsp=3B&nbsp=3B <br>> > 0.00000e+00&nbsp=3B&nbsp=<br>> > > =3B <br>> > 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 <br>> > defined:<br>energygrps&nbsp=3B&n=<br>> > > bsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B <br>> > =3D&nbsp=3B =<br>> > > 1CeO 2CeO 3CeO 4CeO<br><br>Someone can help <br>> > me?<br><br>Thanks<br><br>Ph.D. =<br>> > > Osmair V. Oliveira<br>Federal University of Sao Carlos - <br>> > Brazil<br><br /><h=<br>> > > r />Quer uma internet mais segura? <a <br>> > href=3D'http://brasil.microsoft.com.b=<br>> > > <br>> > r/IE8/mergulhe/?utm_source=3DMSN%3BHotmail&utm_medium=3DTagline&utm_campaig=<br>> > > n=3DIE8' target=3D'_new'>Baixe agora o novo Internet Explorer 8. =C9 <br>> > gr=E1t=<br>> > > is!</a></body><br>> > > </html>=<br>> > ><br>> > > --_501ba45b-9607-437c-8b28-bab65219d4e2_--<br>> > ><br>> > ><br>> > ><br>> > > -------------------------------------------------------------------<br>> > > -------------------------------------------------------------------<br>> > > Forschungszentrum Juelich GmbH<br>> > > 52425 Juelich<br>> > ><br>> > > Sitz der Gesellschaft: Juelich<br>> > > Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. 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Clique aqui! <br>> > <http://www.windowslive.com.br><br>> > <br>> > <br>> > ------------------------------------------------------------------------<br>> > <br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the <br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />Quer uma internet mais segura? <a href='http://brasil.microsoft.com.br/IE8/mergulhe/?utm_source=MSN%3BHotmail&utm_medium=Tagline&utm_campaign=IE8' target='_new'>Baixe agora o novo Internet Explorer 8. É grátis!</a></body>
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