On Thu, Jan 28, 2010, Hugh Heldenbrand wrote:
> It seemed strange that only one of my nucleobases would be unstable, so
> I tried redoing some of my other older nucleobase calculations with the
> newer code. I do see differences in energy between the newer code and
> older code. In one case, the simulations produced the same output for
> the first 1500 fs or so, then I started to see differences in energy in
> the fourth decimal place. By 70 ps, the newer code energy is -8211 and
> the older code energy is -8260.
This is probably exactly what you would expect, even if you just compiled
the exact same code with two different compilers. See section 1.3.4 of the
Amber10 users' manual for a discussion of this.
It is certainly possible that some weird behavior happens with softcore TI
at exactly lambda=0 or lambda=1. You can check that by comparing a standard
calculation (with a single prmtop file) vs. a TI calculation that has two
prmtop files.
....dac
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Received on Fri Jan 29 2010 - 05:30:03 PST
