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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Received on Wed Jan 23 2013 - 12:30:04 PST
