> I watched the movies Bill and i cant find anything
> "strange" goign on. Maybe its something funky with the hydrogens on the
> waters which are hard to see with so many of them.
You may have to go back and save each step to mdcrd to see anything
happening. Additionally, did you look at the specific atoms
mentioned in the shake failure output?
> ...
> So then....... I try going back to 12A buffer no shake and setting Taup =
> 20.0 as I read in another thread in our newsgroup. When I do that the
> simulation stops at about 300 ish psec. I check the output and the pressure
> fluctuates wildly with an NPT simulation.
Wild fluctuation is normal for NPT. No shake is not really
appropriate for simulations with TIP3 water, because the water
model depends on shake to keep the vdw-free H within the O radius
(minimization will sometimes be ok).
Bill
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Received on Mon Oct 11 2010 - 13:30:04 PDT
