[gmx-users] crystals of KCl during simulation

[David van der Spoel]

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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