Rebeca García Fandiño wrote:
Thank you very much, André. Could you please indicate me how could
I use these parameters in Gromacs? I have not seen them included in
ions.itp and I could not find anything in the manual.
Best wishes,
Rebeca.
I would recommend reading the following paper, even though it only is
about NaCl it compares the properties of four different parameter sets,
and IIRC Åqvist's parameters were not so great.
@Article{ Hess2006c,
author = "B. Hess and C. Holm and N. {van der Vegt}",
title = "Osmotic coefficients of atomistic NaCl (aq) force
fields",
journal = "J. Chem. Phys.",
year = 2006,
volume = 124,
pages = 164509,
abstract = "Solvated ions are becoming increasingly important
for (bio)molecular simulations. But there are not
much suitable data to validate the
intermediate-range solution structure that ion-water
force fields produce. We compare six selected
combinations of four biomolecular Na-Cl force fields
and four popular water models by means of effective
ion-ion potentials. First we derive an effective
potential at high dilution from simulations of two
ions in explicit water. At higher ionic
concentration multibody effects will become
important. We propose to capture those by employing
a concentration dependent dielectric
permittivity. With the so obtained effective
potentials we then perform implicit solvent
simulations. We demonstrate that our effective
potentials accurately reproduce ion-ion coordination
numbers and the local structure. They allow us
furthermore to calculate osmotic coefficients that
can be directly compared with experimental data. We
show that the osmotic coefficient is a sensitive and
accurate measure for the effective ion-ion
interactions and the intermediate-range structure of
the solution. It is therefore a suitable and useful
quantity for validating and parametrizing atomistic
ion-water force fields. (c) 2006 American Institute
of Physics. 0021-9606"
}
> Date: Mon, 1 Jun 2009 14:52:35 -0300
> Subject: RE: [gmx-users] crystals of KCl during simulation
> From: [email protected]
> To: [email protected]
>
> Hi Rebeca,
>
> I found out a few years ago that OPLS parameters for Na+ were inadequate
> for my simulations on surfactants aggregation due to the formation of
> stable (and unrealistic) ionic bridges. I got better structures using
> Aqvist's parameters (available in GROMACS), maybe you could try these
> parameters for K+ as well.
>
> please let me know if that works.
>
> best regards,
>
> André
>
>
> >
> > Yes, I use PME.
> >
> >> Date: Mon, 1 Jun 2009 19:34:27 +0200
> >> From: [email protected]
> >> To: [email protected]
> >> Subject: Re: [gmx-users] crystals of KCl during simulation
> >>
> >> Rebeca García Fandiño wrote:
> >> > Thank you very much for your answer. I have read some recent
> >> literature,
> >> > and you are right, it is a problem about the parameters for ions in
> >> Amber.
> >> >
> >> > I have found this paper:
> >> > Parameters of Monovalent Ions in the Amber-99 Forcefield:
Assesment of
> >> > Inaccuracies and Proposed Improvements
> >> > http://pubs.acs.org/doi/abs/10.1021/jp0765392
> >> >
> >> > There, they simulate nucleic acids using a combination of Amber and
> >> > OPLS sigma and epsilon for the ions. I have tried that in the
case of
> >> my
> >> > protein, just changing the ion sigma and epsilon in the topology by
> >> > those corresponding to OPLS, but I still observe aggregation for the
> >> ions.
> >> >
> >> > Would this combination of Amber and OPLS have any kind of potential
> >> > problem during the simulation? Has anybody any idea to avoid
this type
> >> > of artefact?
> >>
> >> Just checking, do you use PME? (You should...)
> >> >
> >> > Thank you very much in advance,
> >> >
> >> > Rebeca.
> >> >
> >> > > To: [email protected]
> >> > > Subject: Re: [gmx-users] crystals of KCl during simulation
> >> > > Date: Mon, 1 Jun 2009 14:34:55 +0200
> >> > > From: [email protected]
> >> > >
> >> > >
> >> > > Hi,
> >> > >
> >> > > [email protected] said:
> >> > > >> [..] but after equilibration I have observed that KCl is
> >> > aggregating, like
> >> > > >> if it was making crystals. When I used NaCl instead KCl,
this not
> >> > > >> happened.
> >> > >
> >> > > >> Does anybody has any idea about the reason of the behaviour of
> >> KCl in
> >> > > >> the simulation?
> >> > >
> >> > > This even does happen with Amber :) So my guess is you correctly
> >> > transferred
> >> > > the parameters, but stumbled upon an artefact. If you check the
> >> recent
> >> > > literature you may notice that many publications with Amber
using K+
> >> > > only employ minimal (neutralising) salt conditions as a
workaround.
> >> At
> >> > > least this is what we did recently [1].
> >> > >
> >> > > Marc Baaden
> >> > >
> >> > > [1] Interactions between neuronal fusion proteins explored by
> >> molecular
> >> > > dynamics, Biophys.J.94, 2008, 3436-3446.
> >> > > http://dx.doi.org/10.1529/biophysj.107.123117
> >> > >
> >> > > --
> >> > > Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris
> >> > > mailto:[email protected] - http://www.baaden.ibpc.fr
> >> > > FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217
> >> > >
> >> > >
> >> > > _______________________________________________
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> >>
> >> --
> >> David.
> >>
________________________________________________________________________
> >> David van der Spoel, PhD, Professor of Biology
> >> Dept. of Cell and Molecular Biology, Uppsala University.
> >> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> >> phone: 46 18 471 4205 fax: 46 18 511 755
> >> [email protected] [email protected] http://folding.bmc.uu.se
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________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[email protected] [email protected] http://folding.bmc.uu.se
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