[gmx-users] Nanoparticles does not interact

Mark Abraham Mark.Abraham at anu.edu.au
Fri May 29 04:12:34 CEST 2009 

osmair oliveira wrote:
> 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

Including your .mdp file and clarifying "I have minimized four 
nanoparticle (with 0.5 nm of distance)" would be helpful. Are there 
atoms in difference particles whose interaction distances are inside 
your cutoffs?

Mark

> 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
>  > Fax: (49)-2461-61-2023
>  > mailto: p.yamin[at]fz-juelich.de
>  > Content-Type: multipart/alternative;
>  > boundary="_501ba45b-9607-437c-8b28-bab65219d4e2_"
>  >
>  >
>  > --_501ba45b-9607-437c-8b28-bab65219d4e2_
>  > Content-Type: text/plain; charset="iso-8859-1"
>  > Content-Transfer-Encoding: quoted-printable
>  >
>  >
>  > 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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>  > --_501ba45b-9607-437c-8b28-bab65219d4e2_
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>  > <html>
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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=
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