[gmx-users] crystals of KCl during simulation

Tue Jun 2 19:01:11 CEST 2009

Thank you very much for your answers. Anyway, if I want to simulate my protein with Amber, would it be a big problem to combine parameter from Amber with parameters from OPLS for water and/or ions?

Best wishes,

Rebeca.

> Date: Tue, 2 Jun 2009 09:51:12 -0300
> Subject: Re: [gmx-users] crystals of KCl during simulation
> From: moura at ufscar.br
> To: gmx-users at gromacs.org
> 
> Hi Rebeca,
> 
> the paper David suggests is certainly more complete, I just compared OPLS
> and Aqvist's parameters for sodium for the specific case of anionic
> micelles. anyway, if want to try the Aqvist's parameters take a look
> inside ffoplsaa.atp file (opls_408 for K+).
> 
> best regards,
> 
> André
> 
> > 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: moura at ufscar.br
> >> > To: gmx-users at gromacs.org
> >> >
> >> > 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: spoel at xray.bmc.uu.se
> >> > >> To: gmx-users at gromacs.org
> >> > >> 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: gmx-users at gromacs.org
> >> > >> > > Subject: Re: [gmx-users] crystals of KCl during simulation
> >> > >> > > Date: Mon, 1 Jun 2009 14:34:55 +0200
> >> > >> > > From: baaden at smplinux.de
> >> > >> > >
> >> > >> > >
> >> > >> > > Hi,
> >> > >> > >
> >> > >> > > regafan at hotmail.com 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:baaden at smplinux.de - 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
> >> > >> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
> >> > >>
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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
> > spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
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> >
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> 
> 
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