> 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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Received on Wed Jan 23 2013 - 17:00:03 PST
