Regarding the solubility, the following paper discusses the topic.
.article{aragones2012solubility,
title={Solubility of NaCl in water by molecular simulation revisited},
author={Aragones, JL and Sanz, E. and Vega, C.},
journal={The Journal of Chemical Physics},
volume={136},
pages={244508},
year={2012}
}
On Thu, Jan 24, 2013 at 5:24 AM, Vlad Cojocaru <
vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> Hi Dan,
>
> Thanks ... Sorry .. Of course, I should have mentioned this and not
> write very brief emails ..
> Of course I am aware of Tom's parameters, I spoke with Tom and others
> and we also read several studies about different sets of parameters ..
>
> After all conversations and reading we decided that Dang parameters
> might be the most suitable for protein-DNA simulations.
>
> However, now we see salt crystals also with these parameters although it
> was reported that they do not form. I just wanted to hear if somebody
> experienced similar issues despite what is documented about these
> parameters ...
>
> Best
> Vlad
>
>
> On 01/23/2013 09:03 PM, Daniel Roe wrote:
> > Hi,
> >
> > Joung and Cheatham did some nice work on this topic:
> >
> > In Suk Joung, and T.E. Cheatham, III. "Determination of alkali and
> > halide monovalent ion parameters for use in explicitly solvated
> > biomolecular simulations." J. Phys. Chem. B 112, 9020-9041 (2008).
> >
> > Their parameters are available for the TIP3P, TIP4Pew, and SPCE water
> > models in AmberTools12 (in $AMBERHOME/dat/leap/parm/frcmod.ionsjc_*
> > files).
> >
> > -Dan
> >
> > On Wed, Jan 23, 2013 at 12:23 PM, Vlad Cojocaru
> > <vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> >> Dear Amber community,
> >>
> >> Recently we are observing the formation of KCl crystals in simulations
> >> of about 100 ns with 100 mM KCl. We are using KCl to reproduce the
> >> experiments we are trying to compare with. For these simulations, we
> >> used the Dang parameters for ions as those were reported to not lead to
> >> the formation of salt crystals ?
> >>
> >> Did anybody else experienced this ?
> >>
> >> Best wishes
> >> Vlad
> >>
> >> --
> >> Dr. Vlad Cojocaru
> >> Max Planck Institute for Molecular Biomedicine
> >> Department of Cell and Developmental Biology
> >> Röntgenstrasse 20, 48149 Münster, Germany
> >> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> >> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> >> http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
> --
> Dr. Vlad Cojocaru
> Max Planck Institute for Molecular Biomedicine
> Department of Cell and Developmental Biology
> Röntgenstrasse 20, 48149 Münster, Germany
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
>
>
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>
--
Best,
InSuk Joung
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Received on Wed Jan 23 2013 - 15:30:04 PST
