[gmx-users] Nanoparticles does not interact
osmair oliveira
osmair07 at hotmail.com
Thu May 28 22:28:47 CEST 2009
My *.top file is:
#include "ffoplsaa.itp"
[ moleculetype ]
; Name nrexcl
CeO 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 opls_966 1 CeO O 1 -0.5000 15.9994
....
53 opls_967 1 CeO Ce 2 1.0000 140.116
....
[ bonds ]
53 1 1
...
[ angles ]
53 1 54 1
...
[ system ]
; Name
CeO
[ molecules ]
; Compound #mols
CeO 4
I do not have dihedral parameters and
I don not include [ pairs ] and the cutoff is 0.9 nm
Thans so much.
Osmair
> Date: Thu, 28 May 2009 22:18:32 +0200
> From: p.yamin at fz-juelich.de
> Subject: Re: [gmx-users] Nanoparticles does not interact
> To: gmx-users at gromacs.org
>
> 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
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>
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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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> padding:0px
> }
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> font-size: 10pt=3B
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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> =3B =3B =3B =3B =3B =3B Coul-SR:1CeO-1Ce=
> O =3B =3B 5.84835e+04 =3B =3B 5.43362e+09 =3B =3B 4=
> .45364e+06<br> =3B =3B =3B =3B =3B =3B =3B =
> =3B LJ-SR:1CeO-1CeO =3B =3B 2.26278e+00 =3B =3B 2.10345e+05=
>  =3B -1.26800e+02<br> =3B =3B =3B =3B =3B =3B C=
> oul-SR:1CeO-2CeO =3B =3B 0.00000e+00 =3B =3B 0.00000e+00&nb=
> sp=3B =3B 0.00000e+00<br> =3B =3B =3B =3B =3B =
> =3B =3B =3B LJ-SR:1CeO-2CeO =3B =3B 0.00000e+00 =3B&nbs=
> p=3B 0.00000e+00 =3B =3B 0.00000e+00<br> =3B =3B =3B&nb=
> sp=3B =3B =3B Coul-SR:1CeO-3CeO =3B =3B 0.00000e+00 =3B=
>  =3B 0.00000e+00 =3B =3B 0.00000e+00<br> =3B =3B =
> =3B =3B =3B =3B =3B =3B LJ-SR:1CeO-3CeO =3B =3B=
> 0.00000e+00 =3B =3B 0.00000e+00 =3B =3B 0.00000e+00<br>&nb=
> sp=3B =3B =3B =3B =3B =3B Coul-SR:1CeO-4CeO =3B&nbs=
> p=3B 0.00000e+00 =3B =3B 0.00000e+00 =3B =3B 0.00000e+00<br=
> > =3B =3B =3B =3B =3B =3B =3B =3B LJ-SR:1Ce=
> O-4CeO =3B =3B 0.00000e+00 =3B =3B 0.00000e+00 =3B =
> =3B 0.00000e+00<br> =3B =3B =3B =3B =3B =3B =3B=
> .......<br><br>In my *.mdp file=2C I have defined:<br>energygrps =3B&n=
> bsp=3B =3B =3B =3B =3B =3B =3B =3B =3D =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=
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