[gmx-users] crystals of KCl during simulation
moura at ufscar.br
moura at ufscar.br
Tue Jun 2 14:51:12 CEST 2009
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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> _______________________________________________
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