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: [email protected]
> Subject: Re: [gmx-users] crystals of KCl during simulation
> Date: Mon, 1 Jun 2009 14:34:55 +0200
> From: [email protected]
>
>
> Hi,
>
> [email protected] 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:[email protected] - http://www.baaden.ibpc.fr
> FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217
>
>
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________________________________________________________________________
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
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