> I have recently been working on this and I am still in the testing phase, but these files (attached) should make it possible to use
> the Allner et al. parameters you are referring to.
I haven't tried these new parameters for Mg2+ yet (but we plan too),
however the approach proposed in the Allner et al. paper to get decent
association times for the Mg2+ ions is clever and compelling. I am fairly
confident that these will be better than the current default AMBER-adapted
Aqvist Mg2+ parameters (where we have observed funny artifacts in DNA
simulation such as ions tunneling into the helix leading to base pair
disruption). Jesper's attachments look correct.
--tec3
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Received on Wed May 16 2012 - 12:30:03 PDT
