Dear Dave,
first of all i apologize for the delay in my reply. you are absolutely
right, paramfit was not easy as well and I had to wrote 6 seperate scripts
to run it (beacuse tleap impose command was not able to turn "boron
compounds").
I will re-try mdgx in my leisure time and I will e-mail you this time if I
get confused. Thank you soo much for your valuable answer and time.
All the best,
Erdo
David Cerutti <dscerutti.gmail.com>, 9 Mar 2020 Pzt, 20:37 tarihinde şunu
yazdı:
> 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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Received on Thu Mar 12 2020 - 01:00:02 PDT
