[gmx-users] Nanoparticles does not interact

osmair oliveira osmair07 at hotmail.com
Fri May 29 14:28:13 CEST 2009 

Hi Mark,

My *.mdp file:
cpp                 =  /lib/cpp
integrator          =  md
;constraints         =  h-bonds
dt                  =  0.001
nsteps              =  5000000
nstcomm             =  1
nstxout             =  1000
nstvout             =  1000
nstxtcout           =  100
nstlog              =  1000
nstenergy           =  100
nstlist             =  10
pbc                 =  xyz
ns_type             =  grid
rlist               =  1.0
rvdw                =  1.0
rcoulomb            =  1.0
coulombtype         =  pme    
fourierspacing      =  0.12
pme_order           =  4
energygrps          =  SOL 1CeO 2CeO 3CeO 4CeO 
Tcoupl              =  berendsen
tc-grps             =  system 
ref_t               =   298 
tau_t               =   0.1
pcoupl              =  berendsen
tau_p               =  10.0
compressibility     =  4.5e-5
ref_p               =  1.0
gen_vel             =  no

About clarifying "I have minimized four nanoparticle (with 0.5 nm of distance)".
I build my system inseting four nanoparticles into a box with 7,000 water molecules.
The initial distance between the nanoparticles are 0.5 nm. After 5 ns of simulation
(using the *.mdp file above), this distance is 0.3 nm, sufficiently for interactions
between the nanoparticles. However, these interactions (Coulomb and LJ) are zero.
On the other hand, there are interactions between nanoparticle-water and 
nanoparticle intramolecular. 

I hope that this can help.

Thanks so much,
Osmair
 

> Date: Fri, 29 May 2009 12:12:34 +1000
> From: Mark.Abraham at anu.edu.au
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Nanoparticles does not interact
> 
> 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
> >  >
> >  > _________________________________________________________________
> >  > Emoticons e Winks super diferentes para o Messenger. Baixe agora=2C 
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> >  >
> >  > --_501ba45b-9607-437c-8b28-bab65219d4e2_
> >  > Content-Type: text/html; charset="iso-8859-1"
> >  > Content-Transfer-Encoding: quoted-printable
> >  >
> >  > <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=
> >  > r />Quer uma internet mais segura? <a 
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