Can you point out which part of the tutorial was unclear? I'm not aware of
any Amber tutorials with YouTube support videos, but I can make more
illustrations if that's needed. There are 3-4 stages to the mdgx tutorial
with short summaries at the end of each one, whereas paramfit has about
seven stages. In my view there are fewer moving parts to get snarled in
but if I haven't been concise please let me know where you got confused.
Dave
On Mon, Mar 9, 2020, 8:35 AM Erdem Yeler <erdemyeler.gmail.com> wrote:
> Dear Dave,
> thank you so much for your answer. Actually before paramfit I tried to run
> mdgx but I couldn't understand some parts of tutorial. Some video support
> would be great.
> All the best,
> Erdo
>
> Erdem Yeler <erdemyeler.gmail.com>, 9 Mar 2020 Pzt, 12:10 tarihinde şunu
> yazdı:
>
> > 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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> >> >
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> >>
> >
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Received on Mon Mar 09 2020 - 11:00:01 PDT
