Hi Tom,
We did some careful checking and indeed you were right .. For some
reason the frcmod we were using for the Smith and Dang parameters (see
below) was not overwriting the Aqvist parameters from the parm99.dat ...
Weird is that this is only happening for K+, not for Na+, not for Cl-
(these are correctly overwritten)....
Below is the frcmod we are using .. If you or anybody else has any idea
what could be the problem that this frcmod is not overwriting the
original parm99.dat, please give us a hint ...
Best wishes
Vlad
-------frcmod.ions_dang
smith/dang ion parameters
MASS
IM 35.45 3.235 assumed to be Cl- (ion minus)
IP 22.99 0.250 assumed to be Na+ (ion plus)
Na+ 22.99 0.250 assumed to be Na+ (ion plus)
Cl- 35.45 3.235 assumed to be Cl- (ion minus)
K+ 39.10 1.060 assumed to be K+ (ion plus)
NONB
IM 2.47 0.1 Smith/Dang
IP 1.32 0.13 Smith/Dang
Na+ 1.319 0.13 Smith/Dang
Cl- 2.47 0.1 Smith/Dang
K+ 1.869 0.1 Smith/Dang
On 01/24/2013 09:43 AM, Vlad Cojocaru wrote:
> 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).
>>
>>
>>
>> _______________________________________________
>> 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 Fri Jan 25 2013 - 05:00:02 PST
