On Wed, Feb 10, 2016 at 8:13 AM, Maryam Hamzehee <maryam_h_7860.yahoo.com>
wrote:
> Dear Jason
> Many thanks for your email and reply. I set the igb=6, the problem was
> fixed.
>
This is not a "fix" to your problem, it's part of the debugging process.
Setting igb=6 means you are running the minimization in the gas phase,
which is *very* different from any kind of solution environment. If igb=6
fixes the NaN problem, then there is some kind of problem either with your
GB parameters or your prmtop file.
If you intended to run with some kind of GB model, then changing igb=6 is
the wrong thing to do for your simulation (but a good step in debugging).
Of course, for most things (except perhaps nucleic acids), igb=1 is a poor
model to use in the first place.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Feb 10 2016 - 06:00:05 PST
