Dear Robin,
thank you soo much for your answer. Actually I was worried because I
thought that: if someone takes the parameter from my article (it was
submitted but not published yet) and uses these parameters in paramfit as
an initial value and encounters this result, he/she may refuse my data. But
your answer made me comforted.
Thank you soo much again.
All the best,
Erdem
Robin Betz <robin.robinbetz.com>, 7 Mar 2020 Cmt, 00:08 tarihinde şunu
yazdı:
> 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 Mon Mar 09 2020 - 02:30:02 PDT
