[gmx-users] Nanoparticles does not interact

Thu May 28 22:18:32 CEST 2009

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?

Peyman Yamin
Institut fuer Strukturbiologie und Biophysik (ISB)
ISB-3: Strukturbiochemie
Forschungszentrum Juelich
D-52425 Juelich 
Tel:	(49)-2461-61-2875  
Fax:	(49)-2461-61-2023
mailto: p.yamin[at]fz-juelich.de 
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Hi=2C
I have minimized four nanoparticle (with 0.5 nm of distance)
using the oplsaa force field=2C but the output (*.edr) shows that
the interactions (Coul-SR and LJ-SR) between the nanoparticles are zero=2C
as example:
       Coul-SR:1CeO-1CeO   5.84835e+04   5.43362e+09   4.45364e+06
         LJ-SR:1CeO-1CeO   2.26278e+00   2.10345e+05  -1.26800e+02
       Coul-SR:1CeO-2CeO   0.00000e+00   0.00000e+00   0.00000e+00
         LJ-SR:1CeO-2CeO   0.00000e+00   0.00000e+00   0.00000e+00
       Coul-SR:1CeO-3CeO   0.00000e+00   0.00000e+00   0.00000e+00
         LJ-SR:1CeO-3CeO   0.00000e+00   0.00000e+00   0.00000e+00
       Coul-SR:1CeO-4CeO   0.00000e+00   0.00000e+00   0.00000e+00
         LJ-SR:1CeO-4CeO   0.00000e+00   0.00000e+00   0.00000e+00
        .......

In my *.mdp file=2C I have defined:
energygrps          =3D  1CeO 2CeO 3CeO 4CeO

Someone can help me?

Thanks

Ph.D. Osmair V. Oliveira
Federal University of Sao Carlos - Brazil

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<body class=3D'hmmessage'>
Hi=2C<br>I have minimized four nanoparticle (with 0.5 nm of distance)<br>us=
ing the oplsaa force field=2C but the output (*.edr) shows that<br>the inte=
ractions (Coul-SR and LJ-SR) between the nanoparticles are zero=2C<br>as ex=
ample:<br>&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B Coul-SR:1CeO-1Ce=
O&nbsp=3B&nbsp=3B 5.84835e+04&nbsp=3B&nbsp=3B 5.43362e+09&nbsp=3B&nbsp=3B 4=
.45364e+06<br>&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=
=3B LJ-SR:1CeO-1CeO&nbsp=3B&nbsp=3B 2.26278e+00&nbsp=3B&nbsp=3B 2.10345e+05=
&nbsp=3B -1.26800e+02<br>&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B C=
oul-SR:1CeO-2CeO&nbsp=3B&nbsp=3B 0.00000e+00&nbsp=3B&nbsp=3B 0.00000e+00&nb=
sp=3B&nbsp=3B 0.00000e+00<br>&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=
=3B&nbsp=3B&nbsp=3B LJ-SR:1CeO-2CeO&nbsp=3B&nbsp=3B 0.00000e+00&nbsp=3B&nbs=
p=3B 0.00000e+00&nbsp=3B&nbsp=3B 0.00000e+00<br>&nbsp=3B&nbsp=3B&nbsp=3B&nb=
sp=3B&nbsp=3B&nbsp=3B Coul-SR:1CeO-3CeO&nbsp=3B&nbsp=3B 0.00000e+00&nbsp=3B=
&nbsp=3B 0.00000e+00&nbsp=3B&nbsp=3B 0.00000e+00<br>&nbsp=3B&nbsp=3B&nbsp=
=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B LJ-SR:1CeO-3CeO&nbsp=3B&nbsp=3B=
 0.00000e+00&nbsp=3B&nbsp=3B 0.00000e+00&nbsp=3B&nbsp=3B 0.00000e+00<br>&nb=
sp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B Coul-SR:1CeO-4CeO&nbsp=3B&nbs=
p=3B 0.00000e+00&nbsp=3B&nbsp=3B 0.00000e+00&nbsp=3B&nbsp=3B 0.00000e+00<br=
>&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B LJ-SR:1Ce=
O-4CeO&nbsp=3B&nbsp=3B 0.00000e+00&nbsp=3B&nbsp=3B 0.00000e+00&nbsp=3B&nbsp=
=3B 0.00000e+00<br>&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B=
 .......<br><br>In my *.mdp file=2C I have defined:<br>energygrps&nbsp=3B&n=
bsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B&nbsp=3B =3D&nbsp=3B =
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 /><h=
r />Quer uma internet mais segura? <a href=3D'http://brasil.microsoft.com.b=
r/IE8/mergulhe/?utm_source=3DMSN%3BHotmail&utm_medium=3DTagline&utm_campaig=
n=3DIE8' target=3D'_new'>Baixe agora o novo Internet Explorer 8. =C9 gr=E1t=
is!</a></body>
</html>=

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