Dear Tom,
Thanks a lot for this detailed answer.
To clarify, when talking about Dang parameters, I actually referred to
Smith/Dang, in fact exactly the parameters you wrote. You actually sent
me the parameters a while ago and I also double-checked the original
paper ...
One difference is that we are using TIP3P .... Not sure if this explains
things but maybe we could do a control simulations using SPC-E to check
if we see the same ...
I will also double check with Felipe (the PhD student working with me)
because he actually observed these clusters ...
I'll keep you and the amber list posted
Best wishes
Vlad
On 01/24/2013 01:41 AM, Thomas Cheatham wrote:
>> 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 ?
> Are you sure you are running with what you think you are? Dang parameters
> with Aqvist K+ lead to immediate crystal formation. I do not know about
> Dang K+/Cl- (or if there *is* a Dang K+). However, Smith + Dang appear to
> be fine as has been reported in the ABC simulations and I just looked for
> one of my long trajectories of DNA with KCl Smith/Dang w/
> Lorentz-Bertholet (standard AMBER) combining rules... Parameters are
> (SPC/E water):
>
> Smith / Dang:
>
> RDPARM MENU: printty
> NOTE: if either A or C is zero (*), we cannot infer
> the value of r* or epsilon and assume zero...
>
> Type r* eps
> * HO 0.0000 0.0000
> OH 1.7210 0.2104
> K+ 1.8687 0.1000
> Cl- 2.4700 0.1000
>
> In simulations out to 10 microseconds of DNA in higher KCl salt we do not
> see crystal formation and only transient ion-pairing (very low occupancy
> ~0.25% and short lifetimes). This can be seen in radial distribution
> functions attached. Top is default/old AMBER Aqvist K+ and Dang Cl- which
> immediately forms crystal. Below is the RDF from my DNA simulation...
>
> --tec3
>
> (I haven't checked S+D in TIP3P since we tend to run with Joung parameters
> except for the ABC consortium simulations which use S+D since they were
> run previously; however in TIP4PEW I do not think we see crystals either
> with S+D but I will check).
>
>
>
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--
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 Thu Jan 24 2013 - 01:00:03 PST
