[gmx-users] Nanoparticles does not interact

Mark Abraham Mark.Abraham at anu.edu.au
Fri May 29 15:40:39 CEST 2009


osmair oliveira wrote:
> 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   

With PME, you have short-range forces (which are computed differently 
from the same forces using plain cut-off or RF) and the reciprocal space 
forces (which cannot be decomposed atomwise or groupwise). Perhaps some 
background reading is in order :-)

Mark

> 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>
>  > > > <head>
>  > > > <style>
>  > > > .hmmessage P
>  > > > {
>  > > > margin:0px=3B
>  > > > padding:0px
>  > > > }
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>  > > > font-family:Verdana
>  > > > }
>  > > > </style>
>  > > > </head>
>  > > > <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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