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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Received on Mon Mar 09 2020 - 06:00:03 PDT
