Thanks Andreas! now it's working properly.
and you were right, second derivatives are calculated only for gb=0 or 1.
Andreas Svrcek-Seiler wrote:
> Hi,
>> I'm using the newton and nmode functions of NAB to perform a
>> Newton-Raphson minimization followed by a vibrational frequencies
>> calculation in implicit solvation. When I use the option gb=1, I've
>> found correct GB energy compared with what I've obtained using the
>> Sander module of Amber 8. But when I switch to gb=2, I've got a GB
>> energy really much lower, which gives rise to incorrect frequencies
>> (a lot of them are negative then).
> ...your output shows that the rms gradient is still ~20kcal/(mol A)
> when entering nmode.
> normal modes should be computed at (as close to as possible) a local
> minimum of your energy function. So you should do conjgrad()
> until frms is down to -say- 1.e-3 or even lower before
> tryinng newton-raphson (down to -say- 1.e-10).
> Only then is should be safe to call nmode().
>
> Besides (I believe) the second derivatives are only available for
> gb=1 (though I'm not sure - in doubt read the source)
>
> good luck,
> Andreas
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Received on Wed Nov 14 2007 - 06:07:45 PST
