Hi Erdem,
The reason you get different parameters on re-fit implies that paramfit
hasn't found the global minimum- that is, the best possible parameters.
It may be worth running it a few times until you actually get convergence,
or set the convergence parameters more stringently.
The "bad parameters" warning is pretty aggressive, and just means that the
initial value of the function to minimize is large. That is probably
coming from the value of K, if you're seeing relative energy differences
that are reasonable. K is just a constant offset to discourage the
solver from making dramatic changes in the parameters to account for the
difference in baseline QM and MM energy. In your case, I
wouldn't say the parameters are bad, since as you say, they just got output
as the result of a fit.
It's always a tradeoff when writing scientific codes between warning the
user excessively and creating a black box that appears to give
perfect results all the time. I err on the side of aggressive warnings,
which is why Paramfit yells at you so much.
Hope this helps!
Robin
On Fri, Mar 6, 2020 at 4:12 AM Erdem Yeler <erdemyeler.gmail.com> wrote:
> Hello amberers,
> Let's say I am optimizing X dihedral by using paramfit. After running
> paramfit I obtained fitted.frcmod. And fit_output_energy.out file shows
> that: molecular mechanic energies obtained by using "fitted.frcmod" file
> are, very close to quantum mechanic calculations. No problem so far,
> everything happened as we expected.
> But, when I use fitted.frcmod file as initial parameters and running
> paramfit with these parameters (quantum_A.dat, prmtop and mdcrd files exc..
> are the same, only inital frcmod file was changed), this time
> fit(2)_output_energy.out file says that : my "initial parameters" are very
> far away from quantum mechanic calculations (even if I referenced "relative
> energies" (relative energy on the chart = energy-minimum energy, so there
> is no need to be use Ka)). But how can this happen? Paramfit found some
> parameters and it says these parameters are good but when I re-use them as
> initial, this time how can exactly the same parameters could be "bad
> parameters" as initial? I am really confused. Am I doing something wrong?
> or this result is normal? (I tested many many times).
> Thank you so much...
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Received on Fri Mar 06 2020 - 13:30:02 PST
