[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
> > > =E9 gr=
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> > > >
> > > > --_501ba45b-9607-437c-8b28-bab65219d4e2_
> > > > Content-Type: text/html; charset="iso-8859-1"
> > > > Content-Transfer-Encoding: quoted-printable
> > > >
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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=
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