Thanks Tom. I'll probably submit these to the "Bryce" parameter database one of the following days. I have talked to the author about this.
One way I checked to see if my implementation was correct was to run a single point energy in NAMD of an Mg-Mg system in the gas-phase.
I did this using the parameters in charmm (which they were developed for) and in amber (with the files I attached).
I then checked for a variety of distances that the energies I got were the same (I was both in the repulsive and attractive regions).
I redid the above procedure using the older Roux parameters in charmm as well, just to check that that worked too.
Does that sound like a reasonable test?
Best,
Jesper
On May 16, 2012, at 12:03 PM, Thomas Cheatham III wrote:
>
>> 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 - 12:30:04 PDT
