On Tue, Feb 21, 2012, Aron Broom wrote:
> I'm running a simulation on a system in a vacuum that sadly needs to have a
> net charge. This means the normal PMEMD isn't possible. There is a
> modification of the GB implicit solvent model, igb=6 that is said to do
> exactly this, but unfortunately it isn't currently implemented on the GPU.
> I'm wondering if anyone has thoughts on how bad it would be to simply do
> normal GB (igb=1 or 5 for instance), but set the external dielectric to
> 1.0?
Isn't it pretty easy to just try it and see what you get? You have the
CPU result for vacuum, so you can test both accuracy and timings with what
you propose.
...dac
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Received on Thu Feb 23 2012 - 11:30:03 PST
