[gmx-users] crystals of KCl during simulation
Mark Abraham
Mark.Abraham at anu.edu.au
Wed Jun 3 01:12:19 CEST 2009
Rebeca García Fandiño wrote:
> 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?
Parameters for water might well be the same. Generally speaking, mixing
forcefields is a bad idea. See
http://wiki.gromacs.org/index.php/Parameterization. You might survive
borrowing an ion, but check the literature thoroughly for any reports of
suitable ions, and/or reconsider your force field choice.
Mark
> > 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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> > >> > >> >
> > >> > >> >
> > >>
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> > >> > >> >
> > >> > >> > _______________________________________________
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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
> > >
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> >
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