[gmx-users] crystals of KCl during simulation

[Rebeca García Fandiño]

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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