[gmx-users] crystals of KCl during simulation

Mon Jun 1 20:39:38 CEST 2009

 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.

> 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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